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

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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

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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

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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: Sat Apr 8 06:41:52 2023

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