Cobalt in PDB 3nvl: Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
Enzymatic activity of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
All present enzymatic activity of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei:
5.4.2.1;
Protein crystallography data
The structure of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei, PDB code: 3nvl
was solved by
G.F.Mercaldi,
H.M.Pereira,
A.T.Cordeiro,
A.D.Andricopulo,
O.H.Thiemann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.55 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.670,
85.660,
109.110,
90.00,
102.20,
90.00
|
R / Rfree (%)
|
16.6 /
21.7
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
(pdb code 3nvl). 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 Phosphoglycerate Mutase From Trypanosoma Brucei, PDB code: 3nvl:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 3nvl
Go back to
Cobalt Binding Sites List in 3nvl
Cobalt binding site 1 out
of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co553
b:23.4
occ:1.00
|
OD1
|
A:ASP22
|
1.9
|
26.6
|
1.0
|
OD2
|
A:ASP465
|
2.1
|
21.5
|
1.0
|
OG
|
A:SER74
|
2.2
|
33.3
|
1.0
|
NE2
|
A:HIS466
|
2.2
|
28.6
|
1.0
|
CG
|
A:ASP22
|
2.6
|
31.2
|
1.0
|
OD2
|
A:ASP22
|
2.7
|
35.9
|
1.0
|
CD2
|
A:HIS466
|
2.8
|
23.6
|
1.0
|
CG
|
A:ASP465
|
2.9
|
30.2
|
1.0
|
OD1
|
A:ASP465
|
3.0
|
31.4
|
1.0
|
CB
|
A:SER74
|
3.2
|
32.1
|
1.0
|
CA
|
A:SER74
|
3.3
|
27.1
|
1.0
|
CE1
|
A:HIS466
|
3.4
|
27.7
|
1.0
|
NZ
|
A:LYS356
|
3.6
|
29.4
|
1.0
|
N
|
A:SER74
|
3.6
|
22.7
|
1.0
|
O
|
A:HOH695
|
3.9
|
29.5
|
1.0
|
CG
|
A:HIS466
|
4.0
|
22.6
|
1.0
|
OD2
|
A:ASP424
|
4.0
|
29.7
|
1.0
|
CB
|
A:ASP22
|
4.0
|
25.9
|
1.0
|
CG
|
A:ASP424
|
4.1
|
31.8
|
1.0
|
N
|
A:GLY23
|
4.2
|
29.2
|
1.0
|
ND1
|
A:HIS466
|
4.2
|
23.6
|
1.0
|
CB
|
A:ASP465
|
4.3
|
27.7
|
1.0
|
CE
|
A:LYS356
|
4.3
|
26.2
|
1.0
|
C
|
A:ASN73
|
4.4
|
22.1
|
1.0
|
OD1
|
A:ASP424
|
4.4
|
30.1
|
1.0
|
CA
|
A:ASP22
|
4.4
|
28.4
|
1.0
|
CB
|
A:ASP424
|
4.6
|
30.2
|
1.0
|
CE1
|
A:HIS78
|
4.6
|
18.8
|
1.0
|
C
|
A:ASP22
|
4.7
|
27.9
|
1.0
|
C
|
A:SER74
|
4.8
|
25.0
|
1.0
|
CO
|
A:CO554
|
4.8
|
29.7
|
1.0
|
O
|
A:ASN73
|
4.8
|
25.3
|
1.0
|
CA
|
A:GLY23
|
5.0
|
32.0
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 3nvl
Go back to
Cobalt Binding Sites List in 3nvl
Cobalt binding site 2 out
of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co554
b:29.7
occ:1.00
|
NE2
|
A:HIS428
|
2.1
|
19.2
|
1.0
|
NE2
|
A:HIS495
|
2.2
|
31.8
|
1.0
|
OD2
|
A:ASP424
|
2.3
|
29.7
|
1.0
|
OD2
|
A:ASP319
|
2.6
|
53.9
|
1.0
|
O
|
A:HOH695
|
2.6
|
29.5
|
1.0
|
OD1
|
A:ASP319
|
2.8
|
53.4
|
1.0
|
OD1
|
A:ASP424
|
2.8
|
30.1
|
1.0
|
CG
|
A:ASP424
|
2.9
|
31.8
|
1.0
|
CE1
|
A:HIS428
|
2.9
|
23.5
|
1.0
|
CG
|
A:ASP319
|
3.0
|
49.6
|
1.0
|
CE1
|
A:HIS495
|
3.1
|
30.4
|
1.0
|
CD2
|
A:HIS428
|
3.2
|
23.7
|
1.0
|
CD2
|
A:HIS495
|
3.2
|
31.3
|
1.0
|
NZ
|
A:LYS356
|
4.1
|
29.4
|
1.0
|
ND1
|
A:HIS428
|
4.1
|
24.6
|
1.0
|
CE1
|
A:HIS466
|
4.1
|
27.7
|
1.0
|
NE2
|
A:HIS466
|
4.2
|
28.6
|
1.0
|
ND1
|
A:HIS495
|
4.2
|
34.6
|
1.0
|
CG
|
A:HIS428
|
4.2
|
25.0
|
1.0
|
OG
|
A:SER74
|
4.3
|
33.3
|
1.0
|
CG
|
A:HIS495
|
4.3
|
35.9
|
1.0
|
CB
|
A:ASP424
|
4.4
|
30.2
|
1.0
|
CB
|
A:ASP319
|
4.4
|
44.5
|
1.0
|
ND2
|
A:ASN468
|
4.5
|
24.4
|
1.0
|
O
|
A:HOH680
|
4.7
|
51.9
|
1.0
|
O
|
A:HOH597
|
4.7
|
45.6
|
1.0
|
O
|
A:HOH694
|
4.8
|
30.0
|
1.0
|
CO
|
A:CO553
|
4.8
|
23.4
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 3nvl
Go back to
Cobalt Binding Sites List in 3nvl
Cobalt binding site 3 out
of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_03.jpg) Mono view
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co553
b:27.5
occ:1.00
|
OG
|
B:SER74
|
2.0
|
23.2
|
1.0
|
OD1
|
B:ASP22
|
2.0
|
25.0
|
1.0
|
OD1
|
B:ASP465
|
2.0
|
25.9
|
1.0
|
NE2
|
B:HIS466
|
2.2
|
18.4
|
1.0
|
CG
|
B:ASP22
|
2.6
|
25.2
|
1.0
|
OD2
|
B:ASP22
|
2.7
|
26.5
|
1.0
|
CG
|
B:ASP465
|
2.8
|
27.1
|
1.0
|
CD2
|
B:HIS466
|
2.9
|
21.2
|
1.0
|
CB
|
B:SER74
|
3.0
|
22.8
|
1.0
|
OD2
|
B:ASP465
|
3.0
|
24.7
|
1.0
|
CA
|
B:SER74
|
3.2
|
28.5
|
1.0
|
CE1
|
B:HIS466
|
3.3
|
22.6
|
1.0
|
N
|
B:SER74
|
3.5
|
30.5
|
1.0
|
NZ
|
B:LYS356
|
3.7
|
28.6
|
1.0
|
OD2
|
B:ASP424
|
4.0
|
37.7
|
1.0
|
CG
|
B:HIS466
|
4.1
|
24.0
|
1.0
|
CB
|
B:ASP22
|
4.1
|
18.2
|
1.0
|
CG
|
B:ASP424
|
4.2
|
36.6
|
1.0
|
ND1
|
B:HIS466
|
4.2
|
26.8
|
1.0
|
CB
|
B:ASP465
|
4.2
|
25.6
|
1.0
|
N
|
B:GLY23
|
4.3
|
26.2
|
1.0
|
C
|
B:ASN73
|
4.4
|
30.7
|
1.0
|
CE
|
B:LYS356
|
4.4
|
28.7
|
1.0
|
CA
|
B:ASP22
|
4.5
|
25.7
|
1.0
|
CE1
|
B:HIS78
|
4.6
|
29.3
|
1.0
|
C
|
B:SER74
|
4.6
|
30.9
|
1.0
|
CB
|
B:ASP424
|
4.6
|
35.6
|
1.0
|
OD1
|
B:ASP424
|
4.6
|
31.0
|
1.0
|
C
|
B:ASP22
|
4.8
|
27.2
|
1.0
|
O
|
B:ASN73
|
4.9
|
33.5
|
1.0
|
CD
|
B:LYS356
|
4.9
|
29.0
|
1.0
|
ND1
|
B:HIS78
|
4.9
|
26.5
|
1.0
|
CO
|
B:CO554
|
4.9
|
35.1
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 3nvl
Go back to
Cobalt Binding Sites List in 3nvl
Cobalt binding site 4 out
of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_04.jpg) Mono view
![](/pictures/CO/pdb/nv/3nvl-CO-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co554
b:35.1
occ:1.00
|
OD2
|
B:ASP424
|
2.1
|
37.7
|
1.0
|
NE2
|
B:HIS428
|
2.1
|
29.9
|
1.0
|
NE2
|
B:HIS495
|
2.1
|
31.7
|
1.0
|
OD1
|
B:ASP319
|
2.5
|
49.9
|
1.0
|
OD2
|
B:ASP319
|
2.5
|
52.5
|
1.0
|
CG
|
B:ASP319
|
2.7
|
50.5
|
1.0
|
CG
|
B:ASP424
|
2.8
|
36.6
|
1.0
|
OD1
|
B:ASP424
|
2.9
|
31.0
|
1.0
|
CE1
|
B:HIS495
|
3.0
|
33.3
|
1.0
|
CD2
|
B:HIS428
|
3.1
|
29.4
|
1.0
|
CE1
|
B:HIS428
|
3.1
|
33.4
|
1.0
|
CD2
|
B:HIS495
|
3.2
|
30.4
|
1.0
|
O
|
B:HOH612
|
4.0
|
55.4
|
1.0
|
NZ
|
B:LYS356
|
4.0
|
28.6
|
1.0
|
CB
|
B:ASP319
|
4.2
|
48.9
|
1.0
|
ND1
|
B:HIS495
|
4.2
|
37.6
|
1.0
|
ND1
|
B:HIS428
|
4.2
|
36.5
|
1.0
|
CG
|
B:HIS428
|
4.2
|
25.4
|
1.0
|
O
|
B:HOH619
|
4.2
|
62.5
|
1.0
|
CB
|
B:ASP424
|
4.3
|
35.6
|
1.0
|
CG
|
B:HIS495
|
4.3
|
31.3
|
1.0
|
CE1
|
B:HIS466
|
4.3
|
22.6
|
1.0
|
NE2
|
B:HIS466
|
4.4
|
18.4
|
1.0
|
OG
|
B:SER74
|
4.4
|
23.2
|
1.0
|
ND2
|
B:ASN468
|
4.7
|
22.3
|
1.0
|
O
|
B:ASP424
|
4.9
|
31.9
|
1.0
|
O
|
B:HOH648
|
4.9
|
30.0
|
1.0
|
CO
|
B:CO553
|
4.9
|
27.5
|
1.0
|
|
Reference:
G.F.Mercaldi,
H.M.Pereira,
A.T.Cordeiro,
P.A.Michels,
O.H.Thiemann.
Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei. Febs J. V. 279 2012 2012.
ISSN: ISSN 1742-464X
PubMed: 22458781
DOI: 10.1111/J.1742-4658.2012.08586.X
Page generated: Tue Jul 30 16:21:20 2024
|