Copper in PDB 1f1g: Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Enzymatic activity of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
All present enzymatic activity of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide:
1.15.1.1;
Protein crystallography data
The structure of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide, PDB code: 1f1g
was solved by
P.J.Hart,
N.L.Ogihara,
H.Liu,
A.M.Nersissian,
J.S.Valentine,
D.Eisenberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.35
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.500,
72.480,
72.470,
109.20,
109.55,
109.21
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1f1g:
The structure of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
(pdb code 1f1g). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide, PDB code: 1f1g:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 1f1g
Go back to
Copper Binding Sites List in 1f1g
Copper binding site 1 out
of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu4001
b:13.0
occ:1.00
|
NE2
|
A:HIS48
|
1.9
|
9.7
|
1.0
|
ND1
|
A:HIS46
|
1.9
|
11.0
|
1.0
|
NE2
|
A:HIS120
|
2.0
|
10.0
|
1.0
|
CE1
|
A:HIS48
|
2.9
|
10.1
|
1.0
|
CE1
|
A:HIS46
|
2.9
|
10.5
|
1.0
|
CD2
|
A:HIS120
|
2.9
|
10.9
|
1.0
|
CG
|
A:HIS46
|
3.0
|
9.9
|
1.0
|
CD2
|
A:HIS48
|
3.0
|
9.3
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
10.1
|
1.0
|
CB
|
A:HIS46
|
3.3
|
11.3
|
1.0
|
NE2
|
A:HIS63
|
3.4
|
11.5
|
1.0
|
CD2
|
A:HIS63
|
3.7
|
12.6
|
1.0
|
O
|
A:HOH3083
|
3.8
|
50.0
|
1.0
|
O
|
A:HOH3075
|
3.9
|
50.0
|
1.0
|
CB
|
A:VAL118
|
3.9
|
9.8
|
1.0
|
ND1
|
A:HIS48
|
4.1
|
9.8
|
1.0
|
NE2
|
A:HIS46
|
4.1
|
11.0
|
1.0
|
CD2
|
A:HIS46
|
4.1
|
10.5
|
1.0
|
N
|
A:HIS46
|
4.1
|
8.7
|
1.0
|
CG1
|
A:VAL118
|
4.1
|
11.0
|
1.0
|
CG
|
A:HIS120
|
4.1
|
10.1
|
1.0
|
ND1
|
A:HIS120
|
4.1
|
10.6
|
1.0
|
CG
|
A:HIS48
|
4.1
|
8.2
|
1.0
|
CA
|
A:HIS46
|
4.2
|
10.3
|
1.0
|
CE1
|
A:HIS63
|
4.2
|
10.5
|
1.0
|
O
|
A:VAL118
|
4.4
|
8.8
|
1.0
|
O
|
A:HIS46
|
4.5
|
10.1
|
1.0
|
C
|
A:HIS46
|
4.6
|
8.8
|
1.0
|
CG
|
A:HIS63
|
4.7
|
9.5
|
1.0
|
CG2
|
A:VAL118
|
4.7
|
10.2
|
1.0
|
C
|
A:VAL118
|
4.9
|
8.1
|
1.0
|
ND1
|
A:HIS63
|
4.9
|
11.0
|
1.0
|
C
|
A:PHE45
|
4.9
|
8.7
|
1.0
|
CA
|
A:VAL118
|
5.0
|
8.6
|
1.0
|
|
Copper binding site 2 out
of 6 in 1f1g
Go back to
Copper Binding Sites List in 1f1g
Copper binding site 2 out
of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu4003
b:13.1
occ:1.00
|
NE2
|
B:HIS203
|
1.9
|
10.0
|
1.0
|
ND1
|
B:HIS201
|
2.0
|
10.9
|
1.0
|
NE2
|
B:HIS275
|
2.0
|
9.4
|
1.0
|
CE1
|
B:HIS203
|
2.8
|
9.8
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
10.3
|
1.0
|
CD2
|
B:HIS275
|
3.0
|
10.2
|
1.0
|
CD2
|
B:HIS203
|
3.0
|
9.3
|
1.0
|
CG
|
B:HIS201
|
3.0
|
9.1
|
1.0
|
CE1
|
B:HIS275
|
3.1
|
10.3
|
1.0
|
CB
|
B:HIS201
|
3.3
|
10.2
|
1.0
|
NE2
|
B:HIS218
|
3.3
|
10.8
|
1.0
|
CD2
|
B:HIS218
|
3.7
|
10.9
|
1.0
|
O
|
B:HOH3077
|
3.8
|
50.0
|
1.0
|
CB
|
B:VAL273
|
3.9
|
9.0
|
1.0
|
ND1
|
B:HIS203
|
4.0
|
10.0
|
1.0
|
CG1
|
B:VAL273
|
4.1
|
10.9
|
1.0
|
CD2
|
B:HIS201
|
4.1
|
11.2
|
1.0
|
NE2
|
B:HIS201
|
4.1
|
9.8
|
1.0
|
CG
|
B:HIS203
|
4.1
|
9.1
|
1.0
|
N
|
B:HIS201
|
4.1
|
8.1
|
1.0
|
CG
|
B:HIS275
|
4.2
|
9.2
|
1.0
|
ND1
|
B:HIS275
|
4.2
|
10.2
|
1.0
|
CE1
|
B:HIS218
|
4.2
|
11.2
|
1.0
|
CA
|
B:HIS201
|
4.2
|
8.9
|
1.0
|
O
|
B:VAL273
|
4.4
|
9.6
|
1.0
|
O
|
B:HIS201
|
4.6
|
10.4
|
1.0
|
C
|
B:HIS201
|
4.7
|
9.2
|
1.0
|
CG
|
B:HIS218
|
4.7
|
9.9
|
1.0
|
CG2
|
B:VAL273
|
4.7
|
10.4
|
1.0
|
C
|
B:VAL273
|
4.9
|
8.8
|
1.0
|
ND1
|
B:HIS218
|
4.9
|
10.0
|
1.0
|
CA
|
B:VAL273
|
5.0
|
8.4
|
1.0
|
C
|
B:PHE200
|
5.0
|
9.3
|
1.0
|
|
Copper binding site 3 out
of 6 in 1f1g
Go back to
Copper Binding Sites List in 1f1g
Copper binding site 3 out
of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu4005
b:13.1
occ:1.00
|
NE2
|
C:HIS358
|
2.0
|
9.4
|
1.0
|
ND1
|
C:HIS356
|
2.0
|
11.7
|
1.0
|
NE2
|
C:HIS430
|
2.0
|
10.1
|
1.0
|
CE1
|
C:HIS358
|
2.9
|
9.8
|
1.0
|
CD2
|
C:HIS430
|
3.0
|
10.4
|
1.0
|
CE1
|
C:HIS356
|
3.0
|
11.6
|
1.0
|
CD2
|
C:HIS358
|
3.0
|
9.2
|
1.0
|
CG
|
C:HIS356
|
3.0
|
9.7
|
1.0
|
CE1
|
C:HIS430
|
3.1
|
10.5
|
1.0
|
CB
|
C:HIS356
|
3.3
|
11.4
|
1.0
|
NE2
|
C:HIS373
|
3.3
|
11.4
|
1.0
|
CD2
|
C:HIS373
|
3.7
|
13.7
|
1.0
|
CB
|
C:VAL428
|
3.9
|
9.5
|
1.0
|
O
|
C:HOH3076
|
3.9
|
50.0
|
1.0
|
ND1
|
C:HIS358
|
4.1
|
9.9
|
1.0
|
CG1
|
C:VAL428
|
4.1
|
10.4
|
1.0
|
N
|
C:HIS356
|
4.1
|
8.4
|
1.0
|
NE2
|
C:HIS356
|
4.1
|
11.0
|
1.0
|
CD2
|
C:HIS356
|
4.1
|
11.0
|
1.0
|
CG
|
C:HIS430
|
4.1
|
10.2
|
1.0
|
ND1
|
C:HIS430
|
4.1
|
10.7
|
1.0
|
CG
|
C:HIS358
|
4.1
|
8.6
|
1.0
|
CA
|
C:HIS356
|
4.2
|
10.8
|
1.0
|
CE1
|
C:HIS373
|
4.2
|
10.4
|
1.0
|
O
|
C:VAL428
|
4.3
|
9.3
|
1.0
|
O
|
C:HIS356
|
4.6
|
9.9
|
1.0
|
C
|
C:HIS356
|
4.6
|
9.0
|
1.0
|
CG
|
C:HIS373
|
4.7
|
10.3
|
1.0
|
CG2
|
C:VAL428
|
4.7
|
10.4
|
1.0
|
C
|
C:VAL428
|
4.9
|
8.7
|
1.0
|
ND1
|
C:HIS373
|
4.9
|
12.1
|
1.0
|
CA
|
C:VAL428
|
4.9
|
8.8
|
1.0
|
C
|
C:PHE355
|
5.0
|
8.8
|
1.0
|
|
Copper binding site 4 out
of 6 in 1f1g
Go back to
Copper Binding Sites List in 1f1g
Copper binding site 4 out
of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu4007
b:13.1
occ:1.00
|
NE2
|
D:HIS513
|
1.9
|
10.3
|
1.0
|
ND1
|
D:HIS511
|
2.0
|
9.7
|
1.0
|
NE2
|
D:HIS585
|
2.0
|
9.2
|
1.0
|
CE1
|
D:HIS513
|
2.9
|
9.7
|
1.0
|
CE1
|
D:HIS511
|
2.9
|
10.1
|
1.0
|
CD2
|
D:HIS585
|
3.0
|
10.0
|
1.0
|
CD2
|
D:HIS513
|
3.0
|
9.2
|
1.0
|
CG
|
D:HIS511
|
3.0
|
9.3
|
1.0
|
CE1
|
D:HIS585
|
3.1
|
10.6
|
1.0
|
CB
|
D:HIS511
|
3.3
|
9.9
|
1.0
|
NE2
|
D:HIS528
|
3.3
|
11.8
|
1.0
|
CD2
|
D:HIS528
|
3.6
|
11.2
|
1.0
|
O
|
D:HOH3080
|
3.8
|
50.0
|
1.0
|
O
|
D:HOH3073
|
3.8
|
50.0
|
1.0
|
CB
|
D:VAL583
|
3.9
|
9.0
|
1.0
|
ND1
|
D:HIS513
|
4.0
|
9.6
|
1.0
|
CD2
|
D:HIS511
|
4.1
|
10.7
|
1.0
|
NE2
|
D:HIS511
|
4.1
|
10.5
|
1.0
|
CG1
|
D:VAL583
|
4.1
|
10.4
|
1.0
|
CG
|
D:HIS513
|
4.1
|
8.8
|
1.0
|
N
|
D:HIS511
|
4.1
|
8.8
|
1.0
|
CG
|
D:HIS585
|
4.1
|
9.9
|
1.0
|
ND1
|
D:HIS585
|
4.2
|
10.1
|
1.0
|
CE1
|
D:HIS528
|
4.2
|
11.3
|
1.0
|
CA
|
D:HIS511
|
4.2
|
9.6
|
1.0
|
O
|
D:VAL583
|
4.4
|
9.5
|
1.0
|
O
|
D:HIS511
|
4.6
|
10.8
|
1.0
|
C
|
D:HIS511
|
4.7
|
9.2
|
1.0
|
CG
|
D:HIS528
|
4.7
|
9.8
|
1.0
|
CG2
|
D:VAL583
|
4.7
|
10.4
|
1.0
|
ND1
|
D:HIS528
|
4.9
|
9.8
|
1.0
|
C
|
D:VAL583
|
4.9
|
8.8
|
1.0
|
CA
|
D:VAL583
|
5.0
|
8.6
|
1.0
|
C
|
D:PHE510
|
5.0
|
9.1
|
1.0
|
|
Copper binding site 5 out
of 6 in 1f1g
Go back to
Copper Binding Sites List in 1f1g
Copper binding site 5 out
of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu4009
b:13.1
occ:1.00
|
NE2
|
E:HIS668
|
2.0
|
9.1
|
1.0
|
NE2
|
E:HIS740
|
2.0
|
8.9
|
1.0
|
ND1
|
E:HIS666
|
2.0
|
10.9
|
1.0
|
CE1
|
E:HIS668
|
2.9
|
9.2
|
1.0
|
CD2
|
E:HIS740
|
3.0
|
9.3
|
1.0
|
CE1
|
E:HIS666
|
3.0
|
11.9
|
1.0
|
CD2
|
E:HIS668
|
3.0
|
8.3
|
1.0
|
CG
|
E:HIS666
|
3.0
|
10.5
|
1.0
|
CE1
|
E:HIS740
|
3.0
|
10.2
|
1.0
|
CB
|
E:HIS666
|
3.3
|
11.0
|
1.0
|
NE2
|
E:HIS683
|
3.3
|
11.3
|
1.0
|
CD2
|
E:HIS683
|
3.7
|
12.8
|
1.0
|
O
|
E:HOH3082
|
3.8
|
50.0
|
1.0
|
CB
|
E:VAL738
|
3.9
|
8.9
|
1.0
|
ND1
|
E:HIS668
|
4.1
|
9.4
|
1.0
|
CG1
|
E:VAL738
|
4.1
|
10.5
|
1.0
|
ND1
|
E:HIS740
|
4.1
|
10.8
|
1.0
|
NE2
|
E:HIS666
|
4.1
|
10.4
|
1.0
|
CG
|
E:HIS740
|
4.1
|
9.1
|
1.0
|
N
|
E:HIS666
|
4.1
|
8.8
|
1.0
|
CD2
|
E:HIS666
|
4.1
|
10.4
|
1.0
|
CG
|
E:HIS668
|
4.1
|
8.8
|
1.0
|
CA
|
E:HIS666
|
4.2
|
10.5
|
1.0
|
CE1
|
E:HIS683
|
4.2
|
10.7
|
1.0
|
O
|
E:VAL738
|
4.4
|
8.5
|
1.0
|
O
|
E:HIS666
|
4.6
|
10.2
|
1.0
|
C
|
E:HIS666
|
4.6
|
8.8
|
1.0
|
CG
|
E:HIS683
|
4.7
|
10.4
|
1.0
|
CG2
|
E:VAL738
|
4.8
|
10.4
|
1.0
|
C
|
E:VAL738
|
4.9
|
8.1
|
1.0
|
ND1
|
E:HIS683
|
4.9
|
10.9
|
1.0
|
CA
|
E:VAL738
|
5.0
|
7.9
|
1.0
|
C
|
E:PHE665
|
5.0
|
9.4
|
1.0
|
|
Copper binding site 6 out
of 6 in 1f1g
Go back to
Copper Binding Sites List in 1f1g
Copper binding site 6 out
of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu4011
b:12.9
occ:1.00
|
NE2
|
F:HIS823
|
1.9
|
8.5
|
1.0
|
ND1
|
F:HIS821
|
2.0
|
10.7
|
1.0
|
NE2
|
F:HIS895
|
2.0
|
9.3
|
1.0
|
CE1
|
F:HIS823
|
2.9
|
9.8
|
1.0
|
CD2
|
F:HIS895
|
3.0
|
9.5
|
1.0
|
CE1
|
F:HIS821
|
3.0
|
10.8
|
1.0
|
CD2
|
F:HIS823
|
3.0
|
8.1
|
1.0
|
CG
|
F:HIS821
|
3.0
|
10.5
|
1.0
|
CE1
|
F:HIS895
|
3.0
|
10.5
|
1.0
|
CB
|
F:HIS821
|
3.3
|
10.8
|
1.0
|
NE2
|
F:HIS838
|
3.3
|
11.2
|
1.0
|
CD2
|
F:HIS838
|
3.7
|
11.8
|
1.0
|
O
|
F:HOH3078
|
3.8
|
50.0
|
1.0
|
O
|
F:HOH3081
|
3.9
|
50.0
|
1.0
|
CB
|
F:VAL893
|
3.9
|
9.3
|
1.0
|
ND1
|
F:HIS823
|
4.0
|
9.2
|
1.0
|
CG1
|
F:VAL893
|
4.1
|
10.2
|
1.0
|
CD2
|
F:HIS821
|
4.1
|
11.2
|
1.0
|
NE2
|
F:HIS821
|
4.1
|
10.7
|
1.0
|
CG
|
F:HIS895
|
4.1
|
9.1
|
1.0
|
ND1
|
F:HIS895
|
4.1
|
10.3
|
1.0
|
CG
|
F:HIS823
|
4.1
|
8.3
|
1.0
|
N
|
F:HIS821
|
4.1
|
8.4
|
1.0
|
CE1
|
F:HIS838
|
4.2
|
10.4
|
1.0
|
CA
|
F:HIS821
|
4.2
|
10.2
|
1.0
|
O
|
F:VAL893
|
4.4
|
8.8
|
1.0
|
O
|
F:HIS821
|
4.6
|
10.5
|
1.0
|
C
|
F:HIS821
|
4.7
|
9.4
|
1.0
|
CG
|
F:HIS838
|
4.7
|
10.5
|
1.0
|
CG2
|
F:VAL893
|
4.7
|
9.8
|
1.0
|
C
|
F:VAL893
|
4.9
|
8.9
|
1.0
|
ND1
|
F:HIS838
|
4.9
|
10.5
|
1.0
|
CA
|
F:VAL893
|
4.9
|
8.3
|
1.0
|
C
|
F:PHE820
|
5.0
|
8.7
|
1.0
|
|
Reference:
P.J.Hart,
M.M.Balbirnie,
N.L.Ogihara,
A.M.Nersissian,
M.S.Weiss,
J.S.Valentine,
D.Eisenberg.
A Structure-Based Mechanism For Copper-Zinc Superoxide Dismutase. Biochemistry V. 38 2167 1999.
ISSN: ISSN 0006-2960
PubMed: 10026301
DOI: 10.1021/BI982284U
Page generated: Tue Jul 30 21:46:55 2024
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