Cobalt in PDB 3pjl: The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
Protein crystallography data
The structure of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5, PDB code: 3pjl
was solved by
C.A.Brautigam,
R.K.Deka,
D.R.Tomchick,
M.Machius,
M.V.Norgard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.88 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
34.406,
65.984,
152.374,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.1 /
20.1
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
(pdb code 3pjl). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the
The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5, PDB code: 3pjl:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
Cobalt binding site 1 out
of 7 in 3pjl
Go back to
Cobalt Binding Sites List in 3pjl
Cobalt binding site 1 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-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 The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co186
b:19.6
occ:1.00
|
NE2
|
B:HIS155
|
2.1
|
16.6
|
1.0
|
NE2
|
A:HIS124
|
2.1
|
16.1
|
1.0
|
NE2
|
A:HIS70
|
2.2
|
14.9
|
1.0
|
OE2
|
A:GLU72
|
2.3
|
21.1
|
1.0
|
OE1
|
A:GLU72
|
2.4
|
23.9
|
1.0
|
SD
|
A:MET117
|
2.6
|
17.4
|
1.0
|
CD
|
A:GLU72
|
2.7
|
21.3
|
1.0
|
CE1
|
B:HIS155
|
2.9
|
18.5
|
1.0
|
CE1
|
A:HIS124
|
3.0
|
20.0
|
1.0
|
CD2
|
A:HIS70
|
3.0
|
17.0
|
1.0
|
CD2
|
A:HIS124
|
3.2
|
18.9
|
1.0
|
CE1
|
A:HIS70
|
3.2
|
17.6
|
1.0
|
CD2
|
B:HIS155
|
3.3
|
19.5
|
1.0
|
CG
|
A:MET117
|
3.5
|
17.0
|
1.0
|
CE
|
A:MET117
|
3.7
|
19.7
|
1.0
|
ND1
|
B:HIS155
|
4.1
|
20.4
|
1.0
|
CG
|
A:GLU72
|
4.1
|
25.2
|
1.0
|
ND1
|
A:HIS124
|
4.2
|
19.2
|
1.0
|
CG
|
A:HIS70
|
4.2
|
15.3
|
1.0
|
CG
|
A:HIS124
|
4.3
|
16.2
|
1.0
|
ND1
|
A:HIS70
|
4.3
|
15.7
|
1.0
|
CG
|
B:HIS155
|
4.3
|
21.5
|
1.0
|
O
|
A:HOH270
|
4.5
|
37.3
|
1.0
|
CA
|
A:GLY126
|
4.6
|
17.6
|
1.0
|
CB
|
A:MET117
|
4.9
|
15.3
|
1.0
|
CB
|
A:GLU72
|
4.9
|
18.6
|
1.0
|
|
Cobalt binding site 2 out
of 7 in 3pjl
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Cobalt Binding Sites List in 3pjl
Cobalt binding site 2 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-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 The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co187
b:34.4
occ:0.47
|
NE2
|
B:HIS149
|
2.0
|
61.0
|
1.0
|
O
|
A:HOH304
|
2.0
|
38.4
|
1.0
|
O
|
A:HOH305
|
2.1
|
50.5
|
1.0
|
NE2
|
A:HIS55
|
2.4
|
33.0
|
1.0
|
CE1
|
B:HIS149
|
2.9
|
66.1
|
1.0
|
CD2
|
B:HIS149
|
3.0
|
62.0
|
1.0
|
CE1
|
A:HIS55
|
3.4
|
39.2
|
1.0
|
CD2
|
A:HIS55
|
3.4
|
32.2
|
1.0
|
O
|
B:HOH198
|
4.0
|
22.4
|
1.0
|
ND1
|
B:HIS149
|
4.0
|
66.8
|
1.0
|
CG
|
B:HIS149
|
4.1
|
61.1
|
1.0
|
O
|
A:HOH221
|
4.3
|
22.8
|
1.0
|
ND1
|
A:HIS55
|
4.5
|
37.5
|
1.0
|
CG
|
A:HIS55
|
4.5
|
30.7
|
1.0
|
O
|
B:HOH265
|
4.6
|
36.4
|
1.0
|
O
|
B:HOH249
|
4.8
|
40.0
|
1.0
|
|
Cobalt binding site 3 out
of 7 in 3pjl
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Cobalt Binding Sites List in 3pjl
Cobalt binding site 3 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_03.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-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 The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co186
b:24.8
occ:0.56
|
NE2
|
B:HIS124
|
1.9
|
15.2
|
0.4
|
NE2
|
A:HIS155
|
2.2
|
19.6
|
1.0
|
NE2
|
B:HIS70
|
2.2
|
21.6
|
1.0
|
CD2
|
B:HIS124
|
2.9
|
20.9
|
0.4
|
CE1
|
B:HIS124
|
2.9
|
20.1
|
0.4
|
CE1
|
A:HIS155
|
2.9
|
20.8
|
1.0
|
SD
|
B:MET117
|
3.0
|
21.5
|
1.0
|
CD2
|
B:HIS70
|
3.2
|
27.0
|
1.0
|
CE1
|
B:HIS70
|
3.2
|
22.6
|
1.0
|
OE1
|
B:GLU72
|
3.3
|
51.7
|
1.0
|
CD2
|
A:HIS155
|
3.4
|
21.3
|
1.0
|
CG
|
B:MET117
|
3.6
|
19.5
|
1.0
|
ND1
|
B:HIS124
|
4.0
|
24.0
|
0.4
|
CG
|
B:HIS124
|
4.0
|
22.0
|
0.4
|
ND1
|
A:HIS155
|
4.1
|
21.8
|
1.0
|
CA
|
B:GLY126
|
4.2
|
25.3
|
1.0
|
ND1
|
B:HIS70
|
4.3
|
18.9
|
1.0
|
CG
|
B:HIS70
|
4.3
|
22.3
|
1.0
|
CG
|
A:HIS155
|
4.4
|
18.8
|
1.0
|
CE
|
B:MET117
|
4.4
|
24.8
|
1.0
|
O
|
B:HOH271
|
4.5
|
45.4
|
1.0
|
CD
|
B:GLU72
|
4.5
|
47.6
|
1.0
|
CB
|
B:GLU72
|
4.5
|
33.7
|
1.0
|
CB
|
B:HIS124
|
4.5
|
24.1
|
0.6
|
N
|
B:GLY126
|
4.8
|
21.9
|
1.0
|
ND1
|
B:HIS124
|
4.9
|
31.4
|
0.6
|
C
|
B:GLY126
|
4.9
|
22.1
|
1.0
|
CB
|
B:MET117
|
5.0
|
18.3
|
1.0
|
CG
|
B:HIS124
|
5.0
|
26.5
|
0.6
|
|
Cobalt binding site 4 out
of 7 in 3pjl
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Cobalt Binding Sites List in 3pjl
Cobalt binding site 4 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_04.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-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 The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co187
b:69.0
occ:0.35
|
OD2
|
B:ASP38
|
2.3
|
45.0
|
1.0
|
OD1
|
B:ASP38
|
2.5
|
56.0
|
1.0
|
ND1
|
B:HIS43
|
2.6
|
39.3
|
0.7
|
CG
|
B:ASP38
|
2.7
|
50.4
|
1.0
|
CD2
|
B:HIS43
|
2.8
|
39.8
|
0.3
|
CE1
|
B:HIS43
|
3.4
|
41.7
|
0.7
|
CG
|
B:HIS43
|
3.5
|
36.8
|
0.7
|
CG
|
B:HIS43
|
3.5
|
37.0
|
0.3
|
CB
|
B:HIS43
|
3.7
|
33.6
|
0.3
|
CB
|
B:HIS43
|
3.8
|
33.8
|
0.7
|
CB
|
B:ASN78
|
3.8
|
36.5
|
1.0
|
NE2
|
B:HIS43
|
3.9
|
41.1
|
0.3
|
CB
|
B:ASP38
|
4.2
|
43.5
|
1.0
|
NE2
|
B:HIS43
|
4.4
|
39.6
|
0.7
|
CD2
|
B:HIS43
|
4.5
|
39.0
|
0.7
|
CA
|
B:HIS43
|
4.6
|
28.7
|
0.7
|
ND2
|
B:ASN78
|
4.6
|
33.5
|
1.0
|
CA
|
B:HIS43
|
4.6
|
29.3
|
0.3
|
ND1
|
B:HIS43
|
4.7
|
38.1
|
0.3
|
CG
|
B:ASN78
|
4.8
|
36.6
|
1.0
|
CE1
|
B:HIS43
|
4.9
|
39.4
|
0.3
|
CA
|
B:ASN78
|
4.9
|
33.3
|
1.0
|
|
Cobalt binding site 5 out
of 7 in 3pjl
Go back to
Cobalt Binding Sites List in 3pjl
Cobalt binding site 5 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_05.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co188
b:28.8
occ:0.38
|
O
|
A:HOH192
|
2.2
|
55.6
|
1.0
|
O
|
B:HOH236
|
2.2
|
49.6
|
1.0
|
NE2
|
B:HIS55
|
2.7
|
33.5
|
1.0
|
CD2
|
B:HIS55
|
3.4
|
33.3
|
1.0
|
CE1
|
B:HIS55
|
3.8
|
35.2
|
1.0
|
O
|
A:HOH202
|
4.0
|
20.8
|
1.0
|
O
|
B:HOH200
|
4.2
|
23.6
|
1.0
|
O
|
A:HOH239
|
4.2
|
27.9
|
1.0
|
ND1
|
A:HIS149
|
4.3
|
65.5
|
1.0
|
CE1
|
A:HIS149
|
4.6
|
66.3
|
1.0
|
CG
|
B:HIS55
|
4.6
|
29.8
|
1.0
|
CG
|
B:PRO56
|
4.7
|
34.6
|
1.0
|
O
|
A:HOH283
|
4.7
|
41.3
|
1.0
|
ND1
|
B:HIS55
|
4.8
|
36.3
|
1.0
|
CD
|
B:PRO56
|
4.9
|
30.5
|
1.0
|
O
|
A:HOH282
|
4.9
|
31.2
|
1.0
|
|
Cobalt binding site 6 out
of 7 in 3pjl
Go back to
Cobalt Binding Sites List in 3pjl
Cobalt binding site 6 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_06.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co189
b:73.4
occ:0.44
|
NE2
|
B:HIS43
|
2.4
|
39.6
|
0.7
|
OD2
|
B:ASP36
|
2.4
|
40.1
|
1.0
|
CE1
|
B:HIS43
|
2.5
|
39.4
|
0.3
|
NE2
|
B:HIS43
|
2.6
|
41.1
|
0.3
|
CE1
|
B:HIS43
|
3.1
|
41.7
|
0.7
|
CD2
|
B:HIS43
|
3.4
|
39.0
|
0.7
|
CG
|
B:ASP36
|
3.4
|
40.9
|
1.0
|
ND1
|
B:HIS43
|
3.8
|
38.1
|
0.3
|
CB
|
B:ASP36
|
3.8
|
37.6
|
1.0
|
CD2
|
B:HIS43
|
3.9
|
39.8
|
0.3
|
ND1
|
B:HIS43
|
4.3
|
39.3
|
0.7
|
O
|
B:HOH215
|
4.4
|
51.0
|
1.0
|
CG
|
B:HIS43
|
4.5
|
37.0
|
0.3
|
CG
|
B:HIS43
|
4.5
|
36.8
|
0.7
|
OD1
|
B:ASP36
|
4.6
|
40.8
|
1.0
|
|
Cobalt binding site 7 out
of 7 in 3pjl
Go back to
Cobalt Binding Sites List in 3pjl
Cobalt binding site 7 out
of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_07.jpg) Mono view
![](/pictures/CO/pdb/pj/3pjl-CO-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co190
b:53.0
occ:0.46
|
OD1
|
B:ASP74
|
2.3
|
60.0
|
1.0
|
NE2
|
B:HIS124
|
2.5
|
33.2
|
0.6
|
O
|
B:HOH257
|
2.5
|
41.2
|
1.0
|
CG
|
B:ASP74
|
2.9
|
53.2
|
1.0
|
CD2
|
B:HIS124
|
3.1
|
30.6
|
0.6
|
OD2
|
B:ASP74
|
3.3
|
61.4
|
1.0
|
CE1
|
B:HIS124
|
3.7
|
31.1
|
0.6
|
OD2
|
B:ASP121
|
4.0
|
58.5
|
1.0
|
OE2
|
B:GLU72
|
4.0
|
50.6
|
1.0
|
CB
|
B:ASP74
|
4.0
|
38.1
|
1.0
|
O
|
B:HOH270
|
4.3
|
56.1
|
1.0
|
CG
|
B:HIS124
|
4.4
|
26.5
|
0.6
|
ND1
|
B:HIS124
|
4.6
|
31.4
|
0.6
|
O
|
B:HOH224
|
4.7
|
29.6
|
1.0
|
CG
|
B:ASP121
|
4.7
|
50.6
|
1.0
|
CD
|
B:GLU72
|
5.0
|
47.6
|
1.0
|
|
Reference:
C.A.Brautigam,
R.K.Deka,
Z.Ouyang,
M.Goldberg,
M.Machius,
G.Knutsen,
D.R.Tomchick,
M.V.Norgard.
Characterization of the TP34 Lipoprotein From Treponema Pallidum Suggests A Role in Transition Metal Homeostasis To Be Published.
Page generated: Tue Jul 30 16:25:50 2024
|