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Copper in PDB 1zdq: Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound

Enzymatic activity of Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound

All present enzymatic activity of Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound, PDB code: 1zdq was solved by H.J.Wijma, I.S.Macpherson, M.Alexandre, R.E.M.Diederix, G.W.Canters, M.E.P.Murphy, M.P.Verbeet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.52 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.968, 103.012, 146.903, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound (pdb code 1zdq). 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 MET150GLY Afnir with Methylsulfanyl Methane Bound, PDB code: 1zdq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1zdq

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Copper binding site 1 out of 6 in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound


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 MET150GLY Afnir with Methylsulfanyl Methane Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:18.3
occ:1.00
 ND1 A:HIS145 2.0 14.9 1.0
ND1 A:HIS95 2.1 15.6 1.0
SG A:CYS136 2.3 15.4 1.0
SD A:MET62 2.3 17.8 1.0
CE1 A:HIS145 2.9 16.6 1.0
CE1 A:HIS95 3.0 16.2 1.0
CG A:HIS145 3.1 14.2 1.0
CG A:HIS95 3.2 14.9 1.0
CE A:MET62 3.2 17.4 1.0
CB A:CYS136 3.3 14.7 1.0
CG A:MET62 3.4 17.4 1.0
CB A:HIS145 3.5 13.1 1.0
CB A:HIS95 3.5 16.2 1.0
CA A:HIS95 4.0 16.0 1.0
NE2 A:HIS145 4.1 16.3 1.0
NE2 A:HIS95 4.2 15.2 1.0
CD2 A:HIS145 4.2 15.7 1.0
CB A:MET62 4.2 16.9 1.0
CD2 A:HIS95 4.3 16.0 1.0
CG A:PRO138 4.3 15.5 1.0
O A:MET94 4.3 16.5 1.0
SG1 A:MSM1507 4.5 24.3 1.0
CA A:HIS145 4.7 13.2 1.0
CD A:PRO138 4.7 15.3 1.0
CA A:CYS136 4.7 14.1 1.0
N A:ASN96 4.8 16.5 1.0
C A:HIS95 5.0 16.3 1.0
N A:HIS95 5.0 16.4 1.0

Copper binding site 2 out of 6 in 1zdq

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Copper binding site 2 out of 6 in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound


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 MET150GLY Afnir with Methylsulfanyl Methane Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:17.7
occ:1.00
 O A:HOH1876 2.0 25.7 1.0
NE2 A:HIS100 2.0 13.1 1.0
NE2 B:HIS306 2.0 12.0 1.0
NE2 A:HIS135 2.1 14.6 1.0
O B:HOH1838 2.2 26.9 1.0
CE1 A:HIS100 2.9 15.6 1.0
CE1 B:HIS306 3.0 11.1 1.0
CD2 A:HIS135 3.1 14.3 1.0
CD2 B:HIS306 3.1 12.6 1.0
CD2 A:HIS100 3.1 13.8 1.0
CE1 A:HIS135 3.1 14.7 1.0
OD1 A:ASP98 3.7 24.3 1.0
NE2 B:HIS255 3.8 17.9 1.0
ND1 A:HIS100 4.1 14.0 1.0
CD2 B:HIS255 4.1 17.7 1.0
ND1 B:HIS306 4.1 11.8 1.0
O A:HOH1669 4.2 28.9 1.0
CG B:HIS306 4.2 12.7 1.0
CG A:HIS100 4.2 12.4 1.0
ND1 A:HIS135 4.2 13.7 1.0
CG A:HIS135 4.2 14.3 1.0
CG A:ASP98 4.3 18.5 1.0
CE1 B:HIS255 4.5 16.8 1.0
OD2 A:ASP98 4.5 20.4 1.0
O A:HOH1746 4.8 17.4 1.0
CG B:HIS255 4.8 15.3 1.0
CD2 B:LEU308 5.0 15.0 1.0

Copper binding site 3 out of 6 in 1zdq

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Copper binding site 3 out of 6 in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound


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 MET150GLY Afnir with Methylsulfanyl Methane Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1503

b:22.4
occ:1.00
 ND1 B:HIS145 2.1 19.2 1.0
ND1 B:HIS95 2.1 18.5 1.0
SG B:CYS136 2.2 19.9 1.0
SD B:MET62 2.4 19.7 1.0
CE1 B:HIS145 2.9 19.7 1.0
CE1 B:HIS95 3.1 19.6 1.0
CG B:HIS145 3.1 19.2 1.0
CG B:HIS95 3.1 20.1 1.0
CE B:MET62 3.2 18.8 1.0
CB B:CYS136 3.2 18.5 1.0
CB B:HIS95 3.5 21.3 1.0
CG B:MET62 3.5 19.0 1.0
CB B:HIS145 3.5 18.4 1.0
CA B:HIS95 4.0 21.3 1.0
NE2 B:HIS145 4.1 20.0 1.0
CD2 B:HIS145 4.2 19.8 1.0
NE2 B:HIS95 4.2 18.9 1.0
CD2 B:HIS95 4.2 19.5 1.0
CB B:MET62 4.3 19.5 1.0
CG B:PRO138 4.3 20.2 1.0
O B:MET94 4.3 21.9 1.0
SG1 B:MSM1508 4.6 31.2 1.0
CA B:CYS136 4.7 17.9 1.0
CA B:HIS145 4.7 18.2 1.0
CD B:PRO138 4.7 19.0 1.0
N B:ASN96 4.8 21.1 1.0
N B:HIS95 5.0 22.0 1.0
C B:HIS95 5.0 21.2 1.0

Copper binding site 4 out of 6 in 1zdq

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Copper binding site 4 out of 6 in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound


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 MET150GLY Afnir with Methylsulfanyl Methane Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1504

b:20.6
occ:1.00
 O B:HOH1839 2.0 33.6 1.0
NE2 B:HIS135 2.0 17.6 1.0
NE2 B:HIS100 2.1 17.9 1.0
NE2 C:HIS306 2.1 15.9 1.0
O C:HOH1818 2.3 27.2 1.0
CE1 B:HIS100 3.0 17.9 1.0
CD2 B:HIS135 3.0 16.2 1.0
CE1 C:HIS306 3.0 16.0 1.0
CE1 B:HIS135 3.1 16.5 1.0
CD2 B:HIS100 3.1 16.9 1.0
CD2 C:HIS306 3.2 16.1 1.0
OD1 B:ASP98 3.6 28.9 1.0
NE2 C:HIS255 4.1 19.1 1.0
CE1 C:HIS255 4.1 19.9 1.0
ND1 B:HIS100 4.1 15.9 1.0
O B:HOH1656 4.1 26.3 1.0
ND1 B:HIS135 4.1 16.1 1.0
CG B:HIS135 4.2 16.1 1.0
CG B:ASP98 4.2 23.2 1.0
ND1 C:HIS306 4.2 15.7 1.0
CG B:HIS100 4.2 16.9 1.0
CG C:HIS306 4.3 14.5 1.0
OD2 B:ASP98 4.5 23.4 1.0
CD2 C:HIS255 4.6 18.5 1.0
ND1 C:HIS255 4.7 20.2 1.0
O B:HOH1718 4.8 26.8 1.0
CD2 C:LEU308 4.9 19.4 1.0
CB B:ASP98 4.9 20.6 1.0
CG C:HIS255 5.0 17.7 1.0

Copper binding site 5 out of 6 in 1zdq

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Copper binding site 5 out of 6 in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound


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 MET150GLY Afnir with Methylsulfanyl Methane Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1505

b:26.3
occ:1.00
 ND1 C:HIS145 2.1 23.2 1.0
ND1 C:HIS95 2.2 24.1 1.0
SG C:CYS136 2.2 22.5 1.0
SD C:MET62 2.4 25.5 1.0
CE1 C:HIS145 3.1 21.6 1.0
CG C:HIS145 3.1 21.8 1.0
CG C:HIS95 3.1 25.0 1.0
CE1 C:HIS95 3.1 25.9 1.0
CE C:MET62 3.2 24.9 1.0
CB C:CYS136 3.3 21.6 1.0
CB C:HIS95 3.4 24.8 1.0
CG C:MET62 3.4 24.9 1.0
CB C:HIS145 3.5 21.3 1.0
CA C:HIS95 3.9 24.9 1.0
NE2 C:HIS145 4.2 21.6 1.0
CD2 C:HIS145 4.2 22.8 1.0
NE2 C:HIS95 4.2 24.7 1.0
CD2 C:HIS95 4.3 23.8 1.0
CB C:MET62 4.3 24.2 1.0
O C:MET94 4.3 25.2 1.0
CG C:PRO138 4.3 21.9 1.0
SG1 C:MSM1509 4.5 29.8 1.0
CA C:HIS145 4.7 20.8 1.0
CA C:CYS136 4.7 20.7 1.0
CD C:PRO138 4.7 21.2 1.0
N C:ASN96 4.8 23.7 1.0
N C:HIS95 4.9 25.2 1.0
C C:HIS95 5.0 24.4 1.0

Copper binding site 6 out of 6 in 1zdq

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Copper binding site 6 out of 6 in the Crystal Structure of MET150GLY Afnir with Methylsulfanyl Methane Bound


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 MET150GLY Afnir with Methylsulfanyl Methane Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1506

b:21.9
occ:1.00
 NE2 C:HIS100 2.0 17.0 1.0
NE2 A:HIS306 2.1 16.6 1.0
NE2 C:HIS135 2.1 19.1 1.0
O A:HOH1877 2.3 30.0 1.0
CE1 C:HIS100 2.9 18.2 1.0
CE1 A:HIS306 3.0 16.7 1.0
CD2 C:HIS135 3.0 19.7 1.0
CD2 C:HIS100 3.1 18.4 1.0
CD2 A:HIS306 3.1 17.3 1.0
CE1 C:HIS135 3.2 21.4 1.0
OD1 C:ASP98 3.5 29.9 1.0
CE1 A:HIS255 3.7 23.0 1.0
O C:HOH1655 4.0 32.6 1.0
NE2 A:HIS255 4.1 22.0 1.0
ND1 C:HIS100 4.1 17.7 1.0
ND1 A:HIS306 4.2 16.5 1.0
CG C:HIS100 4.2 18.6 1.0
CG C:HIS135 4.2 20.6 1.0
CG A:HIS306 4.3 15.9 1.0
ND1 C:HIS135 4.3 20.7 1.0
ND1 A:HIS255 4.3 22.5 1.0
CG C:ASP98 4.3 25.1 1.0
OD2 C:ASP98 4.7 27.0 1.0
CD2 A:HIS255 4.8 21.7 1.0
CG1 A:ILE257 4.8 20.8 1.0
O A:HOH1548 4.8 21.3 1.0
CG A:HIS255 4.9 18.6 1.0
CD2 A:LEU308 5.0 18.1 1.0

Reference:

H.J.Wijma, I.Macpherson, M.Alexandre, R.E.Diederix, G.W.Canters, M.E.Murphy, M.P.Verbeet. A Rearranging Ligand Enables Allosteric Control of Catalytic Activity in Copper-Containing Nitrite Reductase. J.Mol.Biol. V. 358 1081 2006.
ISSN: ISSN 0022-2836
PubMed: 16574144
DOI: 10.1016/J.JMB.2006.02.042
Page generated: Mon Jul 14 00:40:18 2025

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