Cobalt in PDB 1t5k: Crystal Structure of Amicyanin Substituted with Cobalt
Protein crystallography data
The structure of Crystal Structure of Amicyanin Substituted with Cobalt, PDB code: 1t5k
was solved by
C.J.Carrell,
X.Wang,
L.Jones,
W.L.Jarrett,
V.L.Davidson,
F.S.Mathews,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
57.70 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.701,
56.401,
58.706,
90.00,
99.67,
90.00
|
R / Rfree (%)
|
18.2 /
21
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Amicyanin Substituted with Cobalt
(pdb code 1t5k). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
Crystal Structure of Amicyanin Substituted with Cobalt, PDB code: 1t5k:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 1t5k
Go back to
Cobalt Binding Sites List in 1t5k
Cobalt binding site 1 out
of 4 in the Crystal Structure of Amicyanin Substituted with Cobalt
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of Amicyanin Substituted with Cobalt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co107
b:13.0
occ:1.00
|
ND1
|
A:HIS95
|
1.9
|
9.0
|
1.0
|
ND1
|
A:HIS53
|
2.1
|
8.7
|
1.0
|
SG
|
A:CYS92
|
2.2
|
9.4
|
1.0
|
O
|
A:HOH780
|
2.3
|
12.7
|
1.0
|
CE1
|
A:HIS95
|
2.8
|
11.8
|
1.0
|
CE1
|
A:HIS53
|
2.9
|
9.2
|
1.0
|
CG
|
A:HIS95
|
3.0
|
9.3
|
1.0
|
CG
|
A:HIS53
|
3.2
|
9.2
|
1.0
|
CB
|
A:CYS92
|
3.5
|
8.1
|
1.0
|
CB
|
A:HIS95
|
3.5
|
8.5
|
1.0
|
O
|
A:PRO52
|
3.6
|
8.2
|
1.0
|
CB
|
A:HIS53
|
3.7
|
7.8
|
1.0
|
CA
|
A:HIS53
|
3.7
|
7.7
|
1.0
|
SD
|
A:MET98
|
3.8
|
9.5
|
1.0
|
NE2
|
A:HIS95
|
4.0
|
11.8
|
1.0
|
CD2
|
A:HIS95
|
4.1
|
10.5
|
1.0
|
NE2
|
A:HIS53
|
4.1
|
8.4
|
1.0
|
CG
|
A:PRO94
|
4.2
|
10.9
|
1.0
|
CD2
|
A:HIS53
|
4.3
|
8.2
|
1.0
|
N
|
A:HIS95
|
4.4
|
9.5
|
1.0
|
CD
|
A:PRO94
|
4.5
|
8.7
|
1.0
|
C
|
A:PRO52
|
4.5
|
8.6
|
1.0
|
CE
|
A:MET98
|
4.6
|
10.2
|
1.0
|
CA
|
A:HIS95
|
4.6
|
8.9
|
1.0
|
N
|
A:HIS53
|
4.6
|
8.3
|
1.0
|
CA
|
A:CYS92
|
4.8
|
7.9
|
1.0
|
N
|
A:ASN54
|
4.8
|
7.6
|
1.0
|
C
|
A:HIS53
|
4.8
|
7.2
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 1t5k
Go back to
Cobalt Binding Sites List in 1t5k
Cobalt binding site 2 out
of 4 in the Crystal Structure of Amicyanin Substituted with Cobalt
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of Amicyanin Substituted with Cobalt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co107
b:14.4
occ:1.00
|
ND1
|
B:HIS95
|
1.9
|
11.0
|
1.0
|
ND1
|
B:HIS53
|
2.0
|
9.2
|
1.0
|
SG
|
B:CYS92
|
2.2
|
9.7
|
1.0
|
O
|
B:HOH778
|
2.3
|
16.1
|
1.0
|
CE1
|
B:HIS95
|
2.8
|
11.8
|
1.0
|
CE1
|
B:HIS53
|
2.9
|
11.9
|
1.0
|
CG
|
B:HIS95
|
3.0
|
9.2
|
1.0
|
CG
|
B:HIS53
|
3.2
|
8.7
|
1.0
|
CB
|
B:CYS92
|
3.5
|
8.5
|
1.0
|
CB
|
B:HIS95
|
3.5
|
9.5
|
1.0
|
CB
|
B:HIS53
|
3.7
|
9.0
|
1.0
|
SD
|
B:MET98
|
3.8
|
12.3
|
1.0
|
O
|
B:PRO52
|
3.8
|
11.0
|
1.0
|
CA
|
B:HIS53
|
3.8
|
8.4
|
1.0
|
NE2
|
B:HIS95
|
4.0
|
12.8
|
1.0
|
CG
|
B:PRO94
|
4.0
|
11.8
|
1.0
|
CD2
|
B:HIS95
|
4.1
|
11.2
|
1.0
|
NE2
|
B:HIS53
|
4.1
|
9.4
|
1.0
|
CD2
|
B:HIS53
|
4.2
|
11.4
|
1.0
|
CD
|
B:PRO94
|
4.4
|
10.9
|
1.0
|
N
|
B:HIS95
|
4.5
|
10.4
|
1.0
|
CE
|
B:MET98
|
4.5
|
13.2
|
1.0
|
CA
|
B:HIS95
|
4.6
|
10.0
|
1.0
|
C
|
B:PRO52
|
4.6
|
9.8
|
1.0
|
N
|
B:HIS53
|
4.7
|
8.9
|
1.0
|
CA
|
B:CYS92
|
4.8
|
8.5
|
1.0
|
N
|
B:ASN54
|
4.9
|
7.9
|
1.0
|
C
|
B:HIS53
|
5.0
|
8.3
|
1.0
|
C
|
B:CYS92
|
5.0
|
8.7
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 1t5k
Go back to
Cobalt Binding Sites List in 1t5k
Cobalt binding site 3 out
of 4 in the Crystal Structure of Amicyanin Substituted with Cobalt
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of Amicyanin Substituted with Cobalt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co107
b:14.4
occ:1.00
|
ND1
|
C:HIS95
|
1.9
|
11.1
|
1.0
|
ND1
|
C:HIS53
|
2.1
|
10.3
|
1.0
|
SG
|
C:CYS92
|
2.2
|
10.2
|
1.0
|
O
|
C:HOH751
|
2.2
|
12.1
|
1.0
|
CE1
|
C:HIS95
|
2.8
|
12.3
|
1.0
|
CE1
|
C:HIS53
|
3.0
|
12.0
|
1.0
|
CG
|
C:HIS95
|
3.0
|
10.1
|
1.0
|
CG
|
C:HIS53
|
3.2
|
9.6
|
1.0
|
CB
|
C:HIS95
|
3.5
|
10.2
|
1.0
|
CB
|
C:CYS92
|
3.5
|
8.6
|
1.0
|
CB
|
C:HIS53
|
3.7
|
9.1
|
1.0
|
O
|
C:PRO52
|
3.7
|
10.0
|
1.0
|
CA
|
C:HIS53
|
3.8
|
8.3
|
1.0
|
SD
|
C:MET98
|
3.8
|
11.2
|
1.0
|
NE2
|
C:HIS95
|
4.0
|
13.2
|
1.0
|
CD2
|
C:HIS95
|
4.1
|
12.0
|
1.0
|
NE2
|
C:HIS53
|
4.1
|
10.5
|
1.0
|
CG
|
C:PRO94
|
4.2
|
12.3
|
1.0
|
CD2
|
C:HIS53
|
4.3
|
8.3
|
1.0
|
N
|
C:HIS95
|
4.4
|
10.4
|
1.0
|
C
|
C:PRO52
|
4.5
|
9.7
|
1.0
|
CD
|
C:PRO94
|
4.6
|
9.5
|
1.0
|
CA
|
C:HIS95
|
4.6
|
10.6
|
1.0
|
N
|
C:HIS53
|
4.6
|
9.2
|
1.0
|
CE
|
C:MET98
|
4.6
|
11.0
|
1.0
|
CA
|
C:CYS92
|
4.8
|
8.3
|
1.0
|
N
|
C:ASN54
|
4.8
|
7.1
|
1.0
|
C
|
C:HIS53
|
4.9
|
8.2
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 1t5k
Go back to
Cobalt Binding Sites List in 1t5k
Cobalt binding site 4 out
of 4 in the Crystal Structure of Amicyanin Substituted with Cobalt
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of Amicyanin Substituted with Cobalt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co107
b:14.7
occ:1.00
|
ND1
|
D:HIS95
|
1.9
|
10.8
|
1.0
|
ND1
|
D:HIS53
|
2.1
|
10.7
|
1.0
|
O
|
D:HOH148
|
2.2
|
11.6
|
1.0
|
SG
|
D:CYS92
|
2.2
|
10.6
|
1.0
|
CE1
|
D:HIS95
|
2.9
|
9.3
|
1.0
|
CE1
|
D:HIS53
|
2.9
|
12.9
|
1.0
|
CG
|
D:HIS95
|
3.0
|
10.2
|
1.0
|
CG
|
D:HIS53
|
3.2
|
11.1
|
1.0
|
CB
|
D:HIS95
|
3.5
|
9.4
|
1.0
|
CB
|
D:CYS92
|
3.5
|
8.9
|
1.0
|
SD
|
D:MET98
|
3.7
|
11.6
|
1.0
|
CB
|
D:HIS53
|
3.7
|
10.3
|
1.0
|
O
|
D:PRO52
|
3.8
|
14.3
|
1.0
|
CA
|
D:HIS53
|
3.9
|
10.2
|
1.0
|
NE2
|
D:HIS95
|
4.0
|
11.5
|
1.0
|
CG
|
D:PRO94
|
4.1
|
10.1
|
1.0
|
NE2
|
D:HIS53
|
4.1
|
12.1
|
1.0
|
CD2
|
D:HIS95
|
4.1
|
12.4
|
1.0
|
CD2
|
D:HIS53
|
4.2
|
12.4
|
1.0
|
CD
|
D:PRO94
|
4.4
|
11.4
|
1.0
|
CE
|
D:MET98
|
4.5
|
14.1
|
1.0
|
N
|
D:HIS95
|
4.5
|
10.7
|
1.0
|
C
|
D:PRO52
|
4.6
|
13.3
|
1.0
|
CA
|
D:HIS95
|
4.6
|
10.3
|
1.0
|
N
|
D:HIS53
|
4.7
|
10.8
|
1.0
|
CA
|
D:CYS92
|
4.8
|
7.8
|
1.0
|
N
|
D:ASN54
|
5.0
|
8.2
|
1.0
|
C
|
D:HIS53
|
5.0
|
9.1
|
1.0
|
|
Reference:
C.J.Carrell,
X.Wang,
L.Jones,
W.L.Jarrett,
V.L.Davidson,
F.S.Mathews.
Crystallographic and uc(Nmr) Investigation of Cobalt-Substituted Amicyanin. Biochemistry V. 43 9381 2004.
ISSN: ISSN 0006-2960
PubMed: 15260481
DOI: 10.1021/BI049635R
Page generated: Tue Jul 30 14:38:34 2024
|