Zinc in PDB 8j2p: Crystal Structure of Pml B-BOX2
Protein crystallography data
The structure of Crystal Structure of Pml B-BOX2, PDB code: 8j2p
was solved by
C.Zhou,
N.Zang,
J.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.38 /
2.09
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
122.55,
122.55,
163.224,
90,
90,
120
|
R / Rfree (%)
|
19.1 /
23.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Pml B-BOX2
(pdb code 8j2p). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Pml B-BOX2, PDB code: 8j2p:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8j2p
Go back to
Zinc Binding Sites List in 8j2p
Zinc binding site 1 out
of 4 in the Crystal Structure of Pml B-BOX2
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Pml B-BOX2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn501
b:43.1
occ:1.00
|
NE2
|
E:HIS194
|
2.1
|
45.5
|
1.0
|
SG
|
E:CYS212
|
2.3
|
46.7
|
1.0
|
SG
|
E:CYS215
|
2.3
|
48.4
|
1.0
|
SG
|
E:CYS189
|
2.3
|
46.0
|
1.0
|
CE1
|
E:HIS194
|
3.0
|
48.2
|
1.0
|
CD2
|
E:HIS194
|
3.0
|
44.0
|
1.0
|
CB
|
E:CYS189
|
3.4
|
43.5
|
1.0
|
CB
|
E:CYS215
|
3.4
|
40.9
|
1.0
|
CB
|
E:CYS212
|
3.5
|
40.5
|
1.0
|
N
|
E:CYS212
|
3.8
|
41.3
|
1.0
|
CB
|
E:ASN191
|
4.0
|
48.9
|
1.0
|
ND1
|
E:HIS194
|
4.1
|
47.4
|
1.0
|
CG
|
E:HIS194
|
4.2
|
49.3
|
1.0
|
CA
|
E:CYS212
|
4.2
|
38.5
|
1.0
|
N
|
E:CYS215
|
4.2
|
38.8
|
1.0
|
CA
|
E:CYS215
|
4.4
|
45.4
|
1.0
|
ND2
|
E:ASN191
|
4.6
|
49.5
|
1.0
|
CA
|
E:CYS189
|
4.8
|
47.9
|
1.0
|
O
|
E:CYS212
|
4.8
|
42.6
|
1.0
|
CG
|
E:ASN191
|
4.8
|
49.4
|
1.0
|
CG2
|
E:THR198
|
4.9
|
42.1
|
1.0
|
C
|
E:CYS212
|
4.9
|
36.8
|
1.0
|
C
|
E:LEU211
|
4.9
|
44.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8j2p
Go back to
Zinc Binding Sites List in 8j2p
Zinc binding site 2 out
of 4 in the Crystal Structure of Pml B-BOX2
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Pml B-BOX2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn502
b:56.1
occ:1.00
|
ND1
|
E:HIS222
|
2.1
|
59.0
|
1.0
|
SG
|
E:CYS204
|
2.3
|
51.7
|
1.0
|
SG
|
E:CYS227
|
2.3
|
87.9
|
1.0
|
SG
|
E:CYS207
|
2.3
|
59.4
|
1.0
|
CE1
|
E:HIS222
|
3.0
|
68.3
|
1.0
|
CG
|
E:HIS222
|
3.1
|
60.8
|
1.0
|
CB
|
E:CYS204
|
3.2
|
48.7
|
1.0
|
CB
|
E:HIS222
|
3.5
|
72.0
|
1.0
|
CB
|
E:CYS207
|
3.7
|
50.7
|
1.0
|
CB
|
E:CYS227
|
3.7
|
83.4
|
1.0
|
N
|
E:CYS207
|
3.9
|
45.1
|
1.0
|
CA
|
E:HIS222
|
3.9
|
79.9
|
1.0
|
NE2
|
E:HIS222
|
4.2
|
71.1
|
1.0
|
CD2
|
E:HIS222
|
4.2
|
63.3
|
1.0
|
CA
|
E:CYS207
|
4.4
|
48.6
|
1.0
|
CA
|
E:CYS204
|
4.6
|
48.1
|
1.0
|
C
|
E:GLY206
|
4.8
|
46.5
|
1.0
|
N
|
E:GLY206
|
4.8
|
50.2
|
1.0
|
CA
|
E:GLY206
|
4.9
|
47.3
|
1.0
|
N
|
E:HIS222
|
4.9
|
84.7
|
1.0
|
CA
|
E:CYS227
|
4.9
|
94.8
|
1.0
|
C
|
E:HIS222
|
4.9
|
90.0
|
1.0
|
C
|
E:CYS204
|
5.0
|
46.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8j2p
Go back to
Zinc Binding Sites List in 8j2p
Zinc binding site 3 out
of 4 in the Crystal Structure of Pml B-BOX2
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Pml B-BOX2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:44.0
occ:1.00
|
NE2
|
A:HIS194
|
2.1
|
48.0
|
1.0
|
SG
|
A:CYS215
|
2.3
|
47.5
|
1.0
|
SG
|
A:CYS212
|
2.3
|
44.8
|
1.0
|
SG
|
A:CYS189
|
2.3
|
44.3
|
1.0
|
CE1
|
A:HIS194
|
3.0
|
46.3
|
1.0
|
CD2
|
A:HIS194
|
3.0
|
44.5
|
1.0
|
CB
|
A:CYS189
|
3.4
|
41.2
|
1.0
|
CB
|
A:CYS215
|
3.4
|
45.4
|
1.0
|
CB
|
A:CYS212
|
3.6
|
40.4
|
1.0
|
N
|
A:CYS212
|
3.8
|
43.1
|
1.0
|
CB
|
A:ASN191
|
4.1
|
52.2
|
1.0
|
ND1
|
A:HIS194
|
4.1
|
47.7
|
1.0
|
CG
|
A:HIS194
|
4.2
|
52.3
|
1.0
|
N
|
A:CYS215
|
4.2
|
37.6
|
1.0
|
CA
|
A:CYS212
|
4.2
|
38.9
|
1.0
|
CA
|
A:CYS215
|
4.4
|
47.7
|
1.0
|
ND2
|
A:ASN191
|
4.7
|
50.6
|
1.0
|
CA
|
A:CYS189
|
4.8
|
45.4
|
1.0
|
O
|
A:CYS212
|
4.8
|
45.2
|
1.0
|
C
|
A:CYS212
|
4.9
|
36.2
|
1.0
|
CG2
|
A:THR198
|
4.9
|
39.7
|
1.0
|
CG
|
A:ASN191
|
4.9
|
52.3
|
1.0
|
C
|
A:LEU211
|
5.0
|
40.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8j2p
Go back to
Zinc Binding Sites List in 8j2p
Zinc binding site 4 out
of 4 in the Crystal Structure of Pml B-BOX2
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/j2/8j2p-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Pml B-BOX2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:55.1
occ:1.00
|
ND1
|
A:HIS222
|
2.1
|
58.1
|
1.0
|
SG
|
A:CYS204
|
2.3
|
51.7
|
1.0
|
SG
|
A:CYS227
|
2.3
|
88.8
|
1.0
|
SG
|
A:CYS207
|
2.3
|
59.9
|
1.0
|
CE1
|
A:HIS222
|
3.0
|
63.6
|
1.0
|
CG
|
A:HIS222
|
3.1
|
65.2
|
1.0
|
CB
|
A:CYS204
|
3.1
|
48.5
|
1.0
|
CB
|
A:HIS222
|
3.5
|
72.2
|
1.0
|
CB
|
A:CYS207
|
3.6
|
50.3
|
1.0
|
N
|
A:CYS207
|
3.9
|
50.7
|
1.0
|
CA
|
A:HIS222
|
4.0
|
80.5
|
1.0
|
CB
|
A:CYS227
|
4.0
|
93.9
|
1.0
|
NE2
|
A:HIS222
|
4.1
|
67.5
|
1.0
|
CD2
|
A:HIS222
|
4.2
|
59.5
|
1.0
|
CA
|
A:CYS207
|
4.3
|
50.4
|
1.0
|
CA
|
A:CYS204
|
4.6
|
42.7
|
1.0
|
C
|
A:GLY206
|
4.9
|
52.8
|
1.0
|
N
|
A:GLY206
|
4.9
|
51.3
|
1.0
|
N
|
A:HIS222
|
5.0
|
80.6
|
1.0
|
C
|
A:CYS204
|
5.0
|
45.6
|
1.0
|
C
|
A:HIS222
|
5.0
|
89.6
|
1.0
|
CA
|
A:GLY206
|
5.0
|
53.5
|
1.0
|
|
Reference:
P.Bercier,
Q.Q.Wang,
N.Zang,
J.Zhang,
C.Yang,
Y.Maimaitiyiming,
M.Abou-Ghali,
C.Berthier,
C.Wu,
M.Niwa-Kawakita,
T.Dirami,
M.C.Geoffroy,
O.Ferhi,
S.Quentin,
S.Benhenda,
Y.Ogra,
Z.Gueroui,
C.Zhou,
H.Naranmandura,
H.De The,
V.Lallemand-Breitenbach.
Structural Basis of Pml/Rara Oncoprotein Targeting By Arsenic Unravels A Cysteine Rheostat Controlling Pml Body Assembly and Function. Cancer Discov 2023.
ISSN: ESSN 2159-8290
PubMed: 37655965
DOI: 10.1158/2159-8290.CD-23-0453
Page generated: Thu Dec 28 13:18:51 2023
|