Zinc in PDB 7zhg: High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop

Other elements in 7zhg:

The structure of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop also contains other interesting chemical elements:

Magnesium (Mg) 90 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop (pdb code 7zhg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop, PDB code: 7zhg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7zhg

Go back to Zinc Binding Sites List in 7zhg
Zinc binding site 1 out of 6 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:37.2
occ:1.00
 SG C:CYS35 2.3 22.4 1.0
SG C:CYS58 2.4 21.0 1.0
SG C:CYS55 2.4 18.4 1.0
SG C:CYS32 2.6 15.3 1.0
CB C:CYS35 3.1 22.4 1.0
CB C:CYS58 3.2 21.0 1.0
CB C:CYS55 3.3 18.4 1.0
CB C:CYS32 3.4 15.3 1.0
N C:CYS58 3.6 21.0 1.0
N C:CYS35 3.8 22.4 1.0
CA C:CYS58 4.0 21.0 1.0
CA C:CYS35 4.1 22.4 1.0
CB C:LYS57 4.5 21.9 1.0
ND2 C:ASN34 4.6 19.9 1.0
N C:GLY36 4.7 19.7 1.0
C C:LYS57 4.7 21.9 1.0
C C:CYS58 4.7 21.0 1.0
CA C:CYS55 4.8 18.4 1.0
N C:GLY59 4.8 17.3 1.0
CB C:ASN34 4.8 19.9 1.0
C C:CYS35 4.8 22.4 1.0
C C:ASN34 4.9 19.9 1.0
CA C:CYS32 4.9 15.3 1.0
N C:LYS57 4.9 21.9 1.0
CA C:LYS57 4.9 21.9 1.0

Zinc binding site 2 out of 6 in 7zhg

Go back to Zinc Binding Sites List in 7zhg
Zinc binding site 2 out of 6 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:34.3
occ:1.00
 SG C:CYS46 2.4 9.1 1.0
SG C:CYS43 2.4 8.6 1.0
SG C:CYS17 2.6 13.2 1.0
SG C:CYS14 2.7 10.5 1.0
CB C:CYS46 3.3 9.1 1.0
CB C:CYS14 3.5 10.5 1.0
CB C:CYS43 3.5 8.6 1.0
CB C:CYS17 3.6 13.2 1.0
N C:CYS17 4.0 13.2 1.0
N C:CYS43 4.1 8.6 1.0
N C:CYS46 4.2 9.1 1.0
CA C:CYS46 4.3 9.1 1.0
CA C:CYS43 4.4 8.6 1.0
CA C:CYS17 4.4 13.2 1.0
CB C:SER16 4.5 12.9 1.0
C C:CYS43 4.9 8.6 1.0
O C:CYS43 4.9 8.6 1.0
CA C:CYS14 4.9 10.5 1.0

Zinc binding site 3 out of 6 in 7zhg

Go back to Zinc Binding Sites List in 7zhg
Zinc binding site 3 out of 6 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:26.8
occ:1.00
 NE2 F:HIS139 2.2 6.3 1.0
SG F:CYS133 2.3 7.2 1.0
SG F:CYS128 2.4 5.4 1.0
SG F:CYS135 2.5 7.8 1.0
CE1 F:HIS139 3.1 6.3 1.0
CD2 F:HIS139 3.3 6.3 1.0
CB F:CYS128 3.5 5.4 1.0
CB F:CYS135 3.7 7.8 1.0
CB F:CYS133 3.7 7.2 1.0
O F:CYS133 3.8 7.2 1.0
N F:CYS135 3.9 7.8 1.0
C F:CYS133 4.0 7.2 1.0
O F:HOH408 4.3 7.3 1.0
ND1 F:HIS139 4.3 6.3 1.0
CA F:CYS135 4.3 7.8 1.0
N F:ARG161 4.4 6.9 1.0
CG F:HIS139 4.4 6.3 1.0
CA F:CYS133 4.5 7.2 1.0
CB F:ARG161 4.5 6.9 1.0
N F:ARG134 4.6 5.8 1.0
CA F:CYS128 4.6 5.4 1.0
NH1 F:ARG161 4.7 6.9 1.0
O F:GLY159 4.8 5.6 1.0
C F:ARG134 4.9 5.8 1.0
CA F:ARG134 4.9 5.8 1.0
CA F:ARG161 4.9 6.9 1.0
C F:CYS135 5.0 7.8 1.0
O F:ARG137 5.0 7.7 1.0

Zinc binding site 4 out of 6 in 7zhg

Go back to Zinc Binding Sites List in 7zhg
Zinc binding site 4 out of 6 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:30.2
occ:1.00
 SG P:CYS24 2.3 12.5 1.0
SG P:CYS42 2.4 9.4 1.0
SG P:CYS21 2.6 12.7 1.0
CB P:CYS39 3.1 11.4 1.0
CB P:CYS42 3.1 9.4 1.0
SG P:CYS39 3.5 11.4 1.0
CB P:CYS24 3.5 12.5 1.0
CB P:CYS21 3.6 12.7 1.0
N P:CYS39 4.0 11.4 1.0
N P:CYS24 4.1 12.5 1.0
CA P:CYS39 4.1 11.4 1.0
N P:CYS42 4.1 9.4 1.0
CA P:CYS42 4.2 9.4 1.0
CA P:CYS24 4.4 12.5 1.0
CB P:ARG23 4.7 13.8 1.0
O2' 2:G1176 4.8 11.3 1.0
C P:CYS39 4.8 11.4 1.0
OE1 P:GLN26 4.9 11.2 1.0
CB P:GLN26 4.9 11.2 1.0
C P:ARG23 4.9 13.8 1.0
O P:CYS39 5.0 11.4 1.0

Zinc binding site 5 out of 6 in 7zhg

Go back to Zinc Binding Sites List in 7zhg
Zinc binding site 5 out of 6 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:35.7
occ:1.00
 SG R:CYS77 2.4 18.2 1.0
SG R:CYS16 2.4 20.1 1.0
CD2 R:HIS24 2.4 15.9 1.0
SG R:CYS21 2.6 13.8 1.0
CB R:CYS77 3.1 18.2 1.0
NE2 R:HIS24 3.2 15.9 1.0
CB R:CYS16 3.4 20.1 1.0
CG R:HIS24 3.6 15.9 1.0
CB R:CYS21 3.7 13.8 1.0
N R:CYS16 4.1 20.1 1.0
CB R:HIS24 4.2 15.9 1.0
N R:CYS77 4.3 18.2 1.0
CA R:CYS77 4.3 18.2 1.0
CA R:CYS16 4.4 20.1 1.0
CE1 R:HIS24 4.4 15.9 1.0
CB R:PRO75 4.5 12.7 1.0
N R:HIS24 4.6 15.9 1.0
ND1 R:HIS24 4.6 15.9 1.0
CB R:TRP23 4.7 14.0 1.0
C R:LYS15 4.8 22.6 1.0
O R:GLU14 4.9 23.7 1.0
CG R:PRO12 5.0 17.2 1.0

Zinc binding site 6 out of 6 in 7zhg

Go back to Zinc Binding Sites List in 7zhg
Zinc binding site 6 out of 6 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn101

b:45.3
occ:1.00
 CB W:CYS23 2.3 28.8 1.0
SG W:CYS42 2.3 26.4 1.0
SG W:CYS20 2.4 24.7 1.0
SG W:CYS39 2.7 22.5 1.0
CB W:CYS20 3.3 24.7 1.0
N W:CYS23 3.4 28.8 1.0
CA W:CYS23 3.4 28.8 1.0
CB W:CYS39 3.5 22.5 1.0
SG W:CYS23 3.5 28.8 1.0
CB W:CYS42 3.7 26.4 1.0
N W:CYS42 4.3 26.4 1.0
C W:CYS23 4.4 28.8 1.0
N W:GLY24 4.5 23.6 1.0
CA W:CYS42 4.5 26.4 1.0
C W:ASP22 4.6 28.0 1.0
CB W:ALA44 4.7 19.3 1.0
CB W:ASN25 4.7 24.5 1.0
CA W:CYS20 4.8 24.7 1.0
N W:ASN25 4.8 24.5 1.0
CA W:CYS39 5.0 22.5 1.0
CB W:ASP22 5.0 28.0 1.0

Reference:

R.Kazan, G.Bourgeois, C.Lazennec-Schurdevin, E.Larquet, Y.Mechulam, P.D.Coureux, E.Schmitt. Role of AIF5B in Archaeal Translation Initiation. Nucleic Acids Res. V. 50 6532 2022.
ISSN: ESSN 1362-4962
PubMed: 35694843
DOI: 10.1093/NAR/GKAC490
Page generated: Wed Oct 30 16:27:49 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy