Cobalt in PDB 1vlx: Structure of Electron Transfer (Cobalt-Protein)
Protein crystallography data
The structure of Structure of Electron Transfer (Cobalt-Protein), PDB code: 1vlx
was solved by
N.Bonander,
T.Vanngard,
L.-C.Tsai,
V.Langer,
H.Nar,
L.Sjolin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.400,
80.400,
110.300,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.5 /
n/a
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Structure of Electron Transfer (Cobalt-Protein)
(pdb code 1vlx). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
Structure of Electron Transfer (Cobalt-Protein), PDB code: 1vlx:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 1vlx
Go back to
Cobalt Binding Sites List in 1vlx
Cobalt binding site 1 out
of 4 in the Structure of Electron Transfer (Cobalt-Protein)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co129
b:2.1
occ:1.00
|
O
|
A:GLY45
|
2.1
|
2.0
|
1.0
|
ND1
|
A:HIS46
|
2.3
|
2.0
|
1.0
|
SG
|
A:CYS112
|
2.4
|
2.4
|
1.0
|
ND1
|
A:HIS117
|
2.4
|
4.3
|
1.0
|
CE1
|
A:HIS46
|
3.0
|
2.0
|
1.0
|
CG
|
A:HIS117
|
3.3
|
3.8
|
1.0
|
C
|
A:GLY45
|
3.3
|
3.7
|
1.0
|
CE1
|
A:HIS117
|
3.4
|
2.0
|
1.0
|
CG
|
A:HIS46
|
3.4
|
5.7
|
1.0
|
CB
|
A:HIS117
|
3.5
|
5.1
|
1.0
|
CA
|
A:HIS46
|
3.5
|
2.0
|
1.0
|
SD
|
A:MET121
|
3.6
|
2.2
|
1.0
|
CB
|
A:CYS112
|
3.6
|
2.3
|
1.0
|
CB
|
A:PHE114
|
3.8
|
2.0
|
1.0
|
N
|
A:HIS46
|
3.8
|
2.0
|
1.0
|
CB
|
A:HIS46
|
3.9
|
2.8
|
1.0
|
NE2
|
A:HIS46
|
4.2
|
4.0
|
1.0
|
CE
|
A:MET121
|
4.4
|
2.0
|
1.0
|
CD2
|
A:HIS46
|
4.4
|
2.0
|
1.0
|
CD2
|
A:HIS117
|
4.4
|
2.0
|
1.0
|
NE2
|
A:HIS117
|
4.5
|
2.0
|
1.0
|
CG
|
A:PHE114
|
4.6
|
2.6
|
1.0
|
CA
|
A:GLY45
|
4.6
|
5.7
|
1.0
|
C
|
A:HIS46
|
4.7
|
2.0
|
1.0
|
N
|
A:ASN47
|
4.8
|
3.1
|
1.0
|
N
|
A:GLY45
|
4.8
|
5.8
|
1.0
|
O
|
A:MET44
|
4.9
|
5.3
|
1.0
|
C
|
A:MET44
|
4.9
|
6.6
|
1.0
|
N
|
A:PHE114
|
5.0
|
2.0
|
1.0
|
CA
|
A:CYS112
|
5.0
|
2.0
|
1.0
|
CD1
|
A:PHE114
|
5.0
|
5.0
|
1.0
|
CA
|
A:HIS117
|
5.0
|
6.9
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 1vlx
Go back to
Cobalt Binding Sites List in 1vlx
Cobalt binding site 2 out
of 4 in the Structure of Electron Transfer (Cobalt-Protein)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co129
b:2.0
occ:1.00
|
ND1
|
B:HIS117
|
2.3
|
6.4
|
1.0
|
SG
|
B:CYS112
|
2.3
|
2.2
|
1.0
|
ND1
|
B:HIS46
|
2.3
|
10.1
|
1.0
|
O
|
B:GLY45
|
2.3
|
2.0
|
1.0
|
CE1
|
B:HIS117
|
3.0
|
8.9
|
1.0
|
CE1
|
B:HIS46
|
3.2
|
11.4
|
1.0
|
CG
|
B:HIS117
|
3.3
|
9.7
|
1.0
|
CA
|
B:HIS46
|
3.3
|
4.3
|
1.0
|
CG
|
B:HIS46
|
3.3
|
9.9
|
1.0
|
C
|
B:GLY45
|
3.4
|
3.4
|
1.0
|
SD
|
B:MET121
|
3.4
|
2.0
|
1.0
|
CB
|
B:CYS112
|
3.5
|
2.0
|
1.0
|
CB
|
B:PHE114
|
3.7
|
2.8
|
1.0
|
CB
|
B:HIS46
|
3.7
|
6.3
|
1.0
|
CB
|
B:HIS117
|
3.7
|
8.8
|
1.0
|
N
|
B:HIS46
|
3.8
|
2.0
|
1.0
|
NE2
|
B:HIS117
|
4.1
|
8.8
|
1.0
|
CD2
|
B:HIS117
|
4.2
|
10.6
|
1.0
|
NE2
|
B:HIS46
|
4.3
|
12.8
|
1.0
|
CE
|
B:MET121
|
4.3
|
2.0
|
1.0
|
CD2
|
B:HIS46
|
4.4
|
11.6
|
1.0
|
CG
|
B:PHE114
|
4.4
|
2.0
|
1.0
|
C
|
B:HIS46
|
4.6
|
2.2
|
1.0
|
N
|
B:ASN47
|
4.7
|
4.5
|
1.0
|
CA
|
B:GLY45
|
4.7
|
4.5
|
1.0
|
CA
|
B:PHE114
|
4.8
|
4.2
|
1.0
|
N
|
B:PHE114
|
4.8
|
3.7
|
1.0
|
N
|
B:GLY45
|
4.9
|
2.0
|
1.0
|
CA
|
B:CYS112
|
4.9
|
2.0
|
1.0
|
O
|
B:MET44
|
4.9
|
5.1
|
1.0
|
CG
|
B:MET121
|
5.0
|
2.0
|
1.0
|
CD1
|
B:PHE114
|
5.0
|
2.0
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 1vlx
Go back to
Cobalt Binding Sites List in 1vlx
Cobalt binding site 3 out
of 4 in the Structure of Electron Transfer (Cobalt-Protein)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co129
b:2.0
occ:1.00
|
ND1
|
C:HIS117
|
2.2
|
2.0
|
1.0
|
O
|
C:GLY45
|
2.2
|
2.0
|
1.0
|
SG
|
C:CYS112
|
2.4
|
2.1
|
1.0
|
ND1
|
C:HIS46
|
2.5
|
2.0
|
1.0
|
CE1
|
C:HIS117
|
3.0
|
2.0
|
1.0
|
CA
|
C:HIS46
|
3.2
|
3.0
|
1.0
|
CG
|
C:HIS117
|
3.3
|
2.0
|
1.0
|
CG
|
C:HIS46
|
3.3
|
3.6
|
1.0
|
C
|
C:GLY45
|
3.3
|
3.1
|
1.0
|
CB
|
C:HIS46
|
3.4
|
2.0
|
1.0
|
CB
|
C:CYS112
|
3.5
|
2.0
|
1.0
|
CE1
|
C:HIS46
|
3.5
|
2.0
|
1.0
|
CB
|
C:HIS117
|
3.7
|
2.0
|
1.0
|
N
|
C:HIS46
|
3.7
|
2.0
|
1.0
|
SD
|
C:MET121
|
3.7
|
2.0
|
1.0
|
CB
|
C:PHE114
|
3.7
|
2.0
|
1.0
|
CE
|
C:MET121
|
3.9
|
2.0
|
1.0
|
NE2
|
C:HIS117
|
4.1
|
2.0
|
1.0
|
CD2
|
C:HIS117
|
4.3
|
3.8
|
1.0
|
C
|
C:HIS46
|
4.4
|
3.6
|
1.0
|
CD2
|
C:HIS46
|
4.5
|
2.0
|
1.0
|
CG
|
C:PHE114
|
4.5
|
3.3
|
1.0
|
NE2
|
C:HIS46
|
4.6
|
2.0
|
1.0
|
N
|
C:ASN47
|
4.6
|
5.5
|
1.0
|
CA
|
C:GLY45
|
4.6
|
4.4
|
1.0
|
O
|
C:MET44
|
4.7
|
3.3
|
1.0
|
N
|
C:PHE114
|
4.8
|
2.6
|
1.0
|
CA
|
C:CYS112
|
4.9
|
3.4
|
1.0
|
N
|
C:GLY45
|
4.9
|
3.8
|
1.0
|
CA
|
C:PHE114
|
4.9
|
2.0
|
1.0
|
C
|
C:MET44
|
5.0
|
2.6
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 1vlx
Go back to
Cobalt Binding Sites List in 1vlx
Cobalt binding site 4 out
of 4 in the Structure of Electron Transfer (Cobalt-Protein)
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co129
b:2.4
occ:1.00
|
O
|
D:GLY45
|
2.2
|
2.0
|
1.0
|
ND1
|
D:HIS117
|
2.3
|
3.2
|
1.0
|
SG
|
D:CYS112
|
2.3
|
5.0
|
1.0
|
ND1
|
D:HIS46
|
2.5
|
4.7
|
1.0
|
CE1
|
D:HIS117
|
3.1
|
2.0
|
1.0
|
CG
|
D:HIS117
|
3.3
|
2.4
|
1.0
|
CE1
|
D:HIS46
|
3.4
|
2.0
|
1.0
|
C
|
D:GLY45
|
3.4
|
2.9
|
1.0
|
CA
|
D:HIS46
|
3.5
|
2.0
|
1.0
|
SD
|
D:MET121
|
3.6
|
2.0
|
1.0
|
CB
|
D:CYS112
|
3.6
|
2.0
|
1.0
|
CB
|
D:PHE114
|
3.6
|
2.0
|
1.0
|
CG
|
D:HIS46
|
3.6
|
2.5
|
1.0
|
CB
|
D:HIS117
|
3.7
|
3.9
|
1.0
|
N
|
D:HIS46
|
3.9
|
2.0
|
1.0
|
CB
|
D:HIS46
|
4.0
|
2.4
|
1.0
|
CE
|
D:MET121
|
4.1
|
3.5
|
1.0
|
NE2
|
D:HIS117
|
4.3
|
2.0
|
1.0
|
CG
|
D:PHE114
|
4.3
|
2.0
|
1.0
|
CD2
|
D:HIS117
|
4.4
|
2.0
|
1.0
|
NE2
|
D:HIS46
|
4.5
|
2.0
|
1.0
|
CA
|
D:GLY45
|
4.7
|
2.0
|
1.0
|
CD2
|
D:HIS46
|
4.7
|
5.2
|
1.0
|
C
|
D:HIS46
|
4.8
|
4.5
|
1.0
|
N
|
D:PHE114
|
4.8
|
5.7
|
1.0
|
CA
|
D:PHE114
|
4.8
|
4.8
|
1.0
|
N
|
D:ASN47
|
4.8
|
5.1
|
1.0
|
O
|
D:MET44
|
4.9
|
6.1
|
1.0
|
CD1
|
D:PHE114
|
4.9
|
2.0
|
1.0
|
CA
|
D:CYS112
|
4.9
|
4.4
|
1.0
|
N
|
D:GLY45
|
5.0
|
2.8
|
1.0
|
CD2
|
D:PHE114
|
5.0
|
2.0
|
1.0
|
C
|
D:MET44
|
5.0
|
5.2
|
1.0
|
|
Reference:
N.Bonander,
T.Vanngard,
L.C.Tsai,
V.Langer,
H.Nar,
L.Sjolin.
The Metal Site of Pseudomonas Aeruginosa Azurin, Revealed By A Crystal Structure Determination of the Co(II) Derivative and Co-Epr Spectroscopy. Proteins V. 27 385 1997.
ISSN: ISSN 0887-3585
PubMed: 9094740
DOI: 10.1002/(SICI)1097-0134(199703)27:3<385::AID-PROT6>3.0.CO;2-C
Page generated: Tue Jul 30 14:42:21 2024
|