Zinc in PDB 5xj2: Structure of Sprlmcd with U747 Rna
Protein crystallography data
The structure of Structure of Sprlmcd with U747 Rna, PDB code: 5xj2
was solved by
Y.Jiang,
Q.Gong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.53 /
2.84
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.384,
94.916,
164.164,
90.00,
95.93,
90.00
|
R / Rfree (%)
|
19.5 /
23.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Sprlmcd with U747 Rna
(pdb code 5xj2). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of Sprlmcd with U747 Rna, PDB code: 5xj2:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5xj2
Go back to
Zinc Binding Sites List in 5xj2
Zinc binding site 1 out
of 4 in the Structure of Sprlmcd with U747 Rna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Sprlmcd with U747 Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:33.0
occ:1.00
|
NH2
|
A:ARG384
|
3.4
|
20.7
|
1.0
|
NE2
|
A:HIS17
|
3.5
|
30.2
|
1.0
|
NE2
|
A:HIS440
|
3.6
|
17.3
|
1.0
|
NE
|
A:ARG384
|
3.7
|
19.1
|
1.0
|
ND2
|
A:ASN409
|
3.7
|
18.3
|
1.0
|
CD2
|
A:HIS441
|
4.0
|
21.8
|
1.0
|
CZ
|
A:ARG384
|
4.0
|
19.8
|
1.0
|
CD2
|
A:HIS440
|
4.1
|
16.5
|
1.0
|
CD2
|
A:HIS17
|
4.2
|
29.7
|
1.0
|
NE2
|
A:HIS441
|
4.4
|
21.8
|
1.0
|
CE1
|
A:HIS17
|
4.5
|
31.9
|
1.0
|
O
|
A:CYS408
|
4.8
|
18.2
|
1.0
|
CD
|
A:ARG384
|
4.8
|
18.1
|
1.0
|
CE1
|
A:HIS440
|
4.8
|
17.0
|
1.0
|
CG
|
A:ASN409
|
4.9
|
18.2
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5xj2
Go back to
Zinc Binding Sites List in 5xj2
Zinc binding site 2 out
of 4 in the Structure of Sprlmcd with U747 Rna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Sprlmcd with U747 Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:45.9
occ:1.00
|
NH2
|
B:ARG384
|
3.2
|
33.4
|
1.0
|
NE2
|
B:HIS17
|
3.3
|
47.4
|
1.0
|
NE2
|
B:HIS440
|
3.4
|
23.0
|
1.0
|
ND1
|
B:HIS441
|
3.5
|
27.2
|
1.0
|
CE1
|
B:HIS441
|
3.6
|
27.8
|
1.0
|
CD2
|
B:HIS440
|
3.8
|
21.9
|
1.0
|
NE
|
B:ARG384
|
3.9
|
32.6
|
1.0
|
CZ
|
B:ARG384
|
4.0
|
33.0
|
1.0
|
CD2
|
B:HIS17
|
4.1
|
44.4
|
1.0
|
CE1
|
B:HIS17
|
4.3
|
47.9
|
1.0
|
ND2
|
B:ASN409
|
4.3
|
33.5
|
1.0
|
CE1
|
B:HIS440
|
4.6
|
23.0
|
1.0
|
CG
|
B:HIS441
|
4.8
|
25.3
|
1.0
|
NE2
|
B:HIS441
|
4.9
|
26.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5xj2
Go back to
Zinc Binding Sites List in 5xj2
Zinc binding site 3 out
of 4 in the Structure of Sprlmcd with U747 Rna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Sprlmcd with U747 Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn501
b:43.8
occ:1.00
|
NH2
|
C:ARG384
|
3.0
|
39.6
|
1.0
|
NE
|
C:ARG384
|
3.5
|
39.5
|
1.0
|
NE2
|
C:HIS17
|
3.6
|
41.3
|
1.0
|
CD2
|
C:HIS441
|
3.7
|
31.5
|
1.0
|
NE2
|
C:HIS440
|
3.7
|
30.8
|
1.0
|
CZ
|
C:ARG384
|
3.7
|
41.0
|
1.0
|
ND2
|
C:ASN409
|
4.0
|
30.6
|
1.0
|
NE2
|
C:HIS441
|
4.1
|
32.9
|
1.0
|
CD2
|
C:HIS440
|
4.2
|
30.0
|
1.0
|
CD2
|
C:HIS17
|
4.5
|
41.0
|
1.0
|
CE1
|
C:HIS17
|
4.6
|
42.9
|
1.0
|
O
|
C:CYS408
|
4.7
|
20.8
|
1.0
|
CD
|
C:ARG384
|
4.8
|
35.9
|
1.0
|
CG
|
C:HIS441
|
4.9
|
31.5
|
1.0
|
CE1
|
C:HIS440
|
4.9
|
28.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5xj2
Go back to
Zinc Binding Sites List in 5xj2
Zinc binding site 4 out
of 4 in the Structure of Sprlmcd with U747 Rna
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Sprlmcd with U747 Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn501
b:42.4
occ:1.00
|
NH1
|
D:ARG384
|
3.1
|
40.6
|
1.0
|
NE2
|
D:HIS440
|
3.4
|
23.2
|
1.0
|
NE2
|
D:HIS17
|
3.5
|
30.0
|
1.0
|
CD2
|
D:HIS441
|
3.8
|
28.4
|
1.0
|
CD2
|
D:HIS440
|
3.9
|
22.2
|
1.0
|
CZ
|
D:ARG384
|
4.0
|
38.3
|
1.0
|
ND2
|
D:ASN409
|
4.1
|
27.4
|
1.0
|
NE2
|
D:HIS441
|
4.2
|
30.8
|
1.0
|
CD2
|
D:HIS17
|
4.2
|
28.6
|
1.0
|
CE1
|
D:HIS17
|
4.5
|
30.0
|
1.0
|
CE1
|
D:HIS440
|
4.6
|
22.9
|
1.0
|
NH2
|
D:ARG384
|
4.7
|
37.2
|
1.0
|
NE
|
D:ARG384
|
4.8
|
36.5
|
1.0
|
O
|
D:CYS408
|
4.9
|
26.2
|
1.0
|
CG
|
D:HIS441
|
5.0
|
26.8
|
1.0
|
CD
|
D:ARG384
|
5.0
|
33.6
|
1.0
|
|
Reference:
Y.Jiang,
F.Li,
J.Wu,
Y.Shi,
Q.Gong.
Structural Insights Into Substrate Selectivity of Ribosomal Rna Methyltransferase Rlmcd Plos One V. 12 85226 2017.
ISSN: ESSN 1932-6203
PubMed: 28949991
DOI: 10.1371/JOURNAL.PONE.0185226
Page generated: Mon Oct 28 15:03:48 2024
|