Zinc in PDB 2xjy: Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form
Protein crystallography data
The structure of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form, PDB code: 2xjy
was solved by
K.El Omari,
D.Karia,
C.Porcher,
E.J.Mancini,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.74 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.140,
54.360,
61.800,
90.00,
95.45,
90.00
|
R / Rfree (%)
|
20.12 /
22.89
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form
(pdb code 2xjy). 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 the LMO2:LDB1-Lid Complex, P21 Crystal Form, PDB code: 2xjy:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2xjy
Go back to
Zinc Binding Sites List in 2xjy
Zinc binding site 1 out
of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:84.9
occ:1.00
|
SG
|
A:CYS33
|
2.2
|
83.2
|
1.0
|
SG
|
A:CYS54
|
2.2
|
72.6
|
1.0
|
ND1
|
A:HIS51
|
2.3
|
73.9
|
1.0
|
SG
|
A:CYS30
|
2.5
|
77.5
|
1.0
|
CB
|
A:CYS33
|
3.1
|
78.9
|
1.0
|
CG
|
A:HIS51
|
3.2
|
72.7
|
1.0
|
CB
|
A:CYS54
|
3.3
|
66.0
|
1.0
|
CB
|
A:CYS30
|
3.3
|
74.6
|
1.0
|
CB
|
A:HIS51
|
3.3
|
67.7
|
1.0
|
CE1
|
A:HIS51
|
3.4
|
74.9
|
1.0
|
N
|
A:CYS33
|
3.9
|
75.2
|
1.0
|
CA
|
A:CYS33
|
4.1
|
77.2
|
1.0
|
N
|
A:HIS51
|
4.2
|
62.6
|
1.0
|
CA
|
A:HIS51
|
4.4
|
65.5
|
1.0
|
CD2
|
A:HIS51
|
4.4
|
76.9
|
1.0
|
NE2
|
A:HIS51
|
4.5
|
77.1
|
1.0
|
CA
|
A:CYS54
|
4.6
|
65.0
|
1.0
|
C
|
A:GLY32
|
4.7
|
76.8
|
1.0
|
CA
|
A:CYS30
|
4.7
|
73.1
|
1.0
|
C
|
A:CYS33
|
4.9
|
82.4
|
1.0
|
N
|
A:CYS54
|
4.9
|
67.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2xjy
Go back to
Zinc Binding Sites List in 2xjy
Zinc binding site 2 out
of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn202
b:56.4
occ:1.00
|
OD2
|
A:ASP83
|
2.1
|
65.1
|
1.0
|
SG
|
A:CYS80
|
2.3
|
44.7
|
1.0
|
SG
|
A:CYS60
|
2.4
|
54.3
|
1.0
|
SG
|
A:CYS57
|
2.4
|
48.9
|
1.0
|
CG
|
A:ASP83
|
3.1
|
56.1
|
1.0
|
CB
|
A:CYS57
|
3.1
|
46.0
|
1.0
|
CB
|
A:CYS60
|
3.4
|
51.7
|
1.0
|
CB
|
A:ASP83
|
3.5
|
43.0
|
1.0
|
CB
|
A:CYS80
|
3.6
|
41.1
|
1.0
|
N
|
A:CYS60
|
3.9
|
51.2
|
1.0
|
N
|
A:CYS80
|
4.2
|
40.9
|
1.0
|
CA
|
A:CYS60
|
4.2
|
52.7
|
1.0
|
OD1
|
A:ASP83
|
4.2
|
55.9
|
1.0
|
SG
|
A:CYS62
|
4.3
|
64.0
|
1.0
|
NH2
|
A:ARG82
|
4.4
|
94.4
|
1.0
|
N
|
A:ASP83
|
4.4
|
40.3
|
1.0
|
CA
|
A:CYS80
|
4.5
|
40.7
|
1.0
|
CA
|
A:ASP83
|
4.6
|
40.1
|
1.0
|
CA
|
A:CYS57
|
4.6
|
46.8
|
1.0
|
CB
|
A:LEU59
|
4.9
|
47.6
|
1.0
|
C
|
A:LEU59
|
4.9
|
53.8
|
1.0
|
N
|
A:GLY61
|
4.9
|
58.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2xjy
Go back to
Zinc Binding Sites List in 2xjy
Zinc binding site 3 out
of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn203
b:53.8
occ:1.00
|
SG
|
A:CYS97
|
2.2
|
57.4
|
1.0
|
ND1
|
A:HIS116
|
2.2
|
52.5
|
1.0
|
SG
|
A:CYS119
|
2.3
|
48.8
|
1.0
|
SG
|
A:CYS94
|
2.5
|
49.4
|
1.0
|
CG
|
A:HIS116
|
3.2
|
49.7
|
1.0
|
CE1
|
A:HIS116
|
3.2
|
52.3
|
1.0
|
CB
|
A:CYS94
|
3.2
|
46.4
|
1.0
|
CB
|
A:CYS119
|
3.3
|
43.8
|
1.0
|
CB
|
A:CYS97
|
3.3
|
54.5
|
1.0
|
CB
|
A:HIS116
|
3.4
|
45.8
|
1.0
|
N
|
A:CYS97
|
3.8
|
52.5
|
1.0
|
N
|
A:HIS116
|
4.1
|
44.4
|
1.0
|
CA
|
A:CYS97
|
4.1
|
54.5
|
1.0
|
NE2
|
A:HIS116
|
4.3
|
52.0
|
1.0
|
CD2
|
A:HIS116
|
4.3
|
51.2
|
1.0
|
CA
|
A:HIS116
|
4.4
|
44.2
|
1.0
|
CA
|
A:CYS119
|
4.7
|
43.8
|
1.0
|
CA
|
A:CYS94
|
4.7
|
46.5
|
1.0
|
CB
|
A:SER96
|
4.8
|
49.2
|
1.0
|
C
|
A:SER96
|
4.9
|
54.8
|
1.0
|
C
|
A:CYS97
|
4.9
|
60.5
|
1.0
|
N
|
A:CYS119
|
5.0
|
45.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2xjy
Go back to
Zinc Binding Sites List in 2xjy
Zinc binding site 4 out
of 4 in the Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the LMO2:LDB1-Lid Complex, P21 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn204
b:44.4
occ:1.00
|
OD2
|
A:ASP147
|
2.1
|
51.1
|
1.0
|
SG
|
A:CYS125
|
2.2
|
42.2
|
1.0
|
SG
|
A:CYS122
|
2.3
|
41.2
|
1.0
|
SG
|
A:CYS144
|
2.3
|
47.0
|
1.0
|
CG
|
A:ASP147
|
3.0
|
47.5
|
1.0
|
CB
|
A:CYS122
|
3.1
|
37.5
|
1.0
|
CB
|
A:CYS125
|
3.2
|
40.3
|
1.0
|
CB
|
A:CYS144
|
3.6
|
41.8
|
1.0
|
N
|
A:CYS125
|
3.6
|
40.3
|
1.0
|
CB
|
A:ASP147
|
3.7
|
41.8
|
1.0
|
OD1
|
A:ASP147
|
3.9
|
47.1
|
1.0
|
CA
|
A:CYS125
|
4.0
|
41.0
|
1.0
|
N
|
A:CYS144
|
4.3
|
41.2
|
1.0
|
CB
|
A:ALA124
|
4.4
|
38.8
|
1.0
|
CA
|
A:CYS144
|
4.5
|
41.0
|
1.0
|
CA
|
A:CYS122
|
4.5
|
37.4
|
1.0
|
C
|
A:ALA124
|
4.8
|
43.8
|
1.0
|
C
|
A:CYS125
|
4.8
|
49.1
|
1.0
|
CB
|
A:LYS127
|
4.9
|
52.3
|
1.0
|
N
|
A:ASP147
|
4.9
|
41.6
|
1.0
|
N
|
A:GLN126
|
4.9
|
46.9
|
1.0
|
CA
|
A:ASP147
|
5.0
|
40.7
|
1.0
|
CA
|
A:ALA124
|
5.0
|
39.0
|
1.0
|
|
Reference:
K.El Omari,
S.J.Hoosdally,
K.Tuladhar,
D.Karia,
P.Vyas,
R.Patient,
C.Porcher,
E.J.Mancini.
Structure of the Leukemia Oncogene LMO2: Implications For the Assembly of A Hematopoietic Transcription Factor Complex. Blood V. 117 2146 2011.
ISSN: ISSN 0006-4971
PubMed: 21076045
DOI: 10.1182/BLOOD-2010-07-293357
Page generated: Thu Oct 17 05:21:17 2024
|