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Zinc in PDB 5gmk: Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution

Other elements in 5gmk:

The structure of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution (pdb code 5gmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution, PDB code: 5gmk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5gmk

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn400

b:30.0
occ:1.00
SG Q:CYS71 2.3 0.0 1.0
SG Q:CYS74 2.3 0.0 1.0
SG Q:CYS13 2.3 0.0 1.0
SG Q:CYS73 2.3 0.0 1.0
CB Q:CYS13 3.0 0.0 1.0
CB Q:CYS74 3.2 0.0 1.0
N Q:CYS74 3.2 0.0 1.0
CB Q:CYS16 3.5 0.0 1.0
N Q:CYS13 3.5 0.0 1.0
CB Q:CYS71 3.7 0.0 1.0
CA Q:CYS74 3.7 0.0 1.0
CA Q:CYS13 3.8 0.0 1.0
CB Q:CYS73 3.9 0.0 1.0
C Q:CYS73 4.1 0.0 1.0
N Q:CYS16 4.3 0.0 1.0
CA Q:CYS73 4.4 0.0 1.0
CG2 Q:ILE12 4.4 0.0 1.0
N Q:CYS73 4.4 0.0 1.0
CA Q:CYS16 4.4 0.0 1.0
SG Q:CYS16 4.6 0.0 1.0
C Q:CYS13 4.6 0.0 1.0
O Q:CYS13 4.7 0.0 1.0
C Q:ILE12 4.7 0.0 1.0
CA Q:CYS71 4.9 0.0 1.0

Zinc binding site 2 out of 7 in 5gmk

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn401

b:30.0
occ:1.00
SG Q:CYS34 2.3 0.0 1.0
SG Q:CYS37 2.3 0.0 1.0
SG Q:CYS64 2.3 0.0 1.0
SG Q:CYS61 2.3 0.0 1.0
CB Q:CYS61 2.9 0.0 1.0
CB Q:CYS37 2.9 0.0 1.0
CB Q:CYS34 3.2 0.0 1.0
CB Q:CYS64 3.4 0.0 1.0
N Q:CYS61 3.7 0.0 1.0
CA Q:CYS61 3.8 0.0 1.0
N Q:CYS37 4.0 0.0 1.0
CA Q:CYS37 4.0 0.0 1.0
CA Q:CYS34 4.5 0.0 1.0
N Q:CYS64 4.5 0.0 1.0
CA Q:CYS64 4.6 0.0 1.0
N Q:CYS34 4.7 0.0 1.0
O Q:LEU39 4.8 0.0 1.0
C Q:CYS37 4.8 0.0 1.0
C Q:ILE60 4.8 0.0 1.0
N Q:THR38 4.8 0.0 1.0
N Q:LEU39 4.9 0.0 1.0

Zinc binding site 3 out of 7 in 5gmk

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn400

b:30.0
occ:1.00
CE1 R:HIS91 2.2 0.0 1.0
SG R:CYS81 2.3 0.0 1.0
SG R:CYS73 2.3 0.0 1.0
NE2 R:HIS91 2.3 0.0 1.0
SG R:CYS87 2.3 0.0 1.0
CB R:CYS81 3.0 0.0 1.0
CB R:CYS73 3.2 0.0 1.0
CB R:CYS87 3.3 0.0 1.0
ND1 R:HIS91 3.5 0.0 1.0
CD2 R:HIS91 3.6 0.0 1.0
CG R:HIS91 4.2 0.0 1.0
N6 E:A35 4.4 0.4 1.0
N R:PHE76 4.5 0.0 1.0
CB R:PHE76 4.5 0.0 1.0
CA R:CYS81 4.5 0.0 1.0
CA R:CYS73 4.6 0.0 1.0
CA R:CYS87 4.7 0.0 1.0
O R:TYR89 4.9 0.0 1.0
CA R:PHE76 5.0 0.0 1.0

Zinc binding site 4 out of 7 in 5gmk

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:0.0
occ:1.00
CB T:CYS104 2.2 0.0 1.0
SG T:CYS148 2.3 0.0 1.0
SG T:CYS105 2.3 0.0 1.0
SG T:CYS108 2.3 0.0 1.0
SG T:CYS104 2.3 0.0 1.0
CB T:CYS148 3.1 0.0 1.0
CB T:CYS105 3.3 0.0 1.0
CA T:CYS104 3.6 0.0 1.0
N T:CYS105 3.7 0.0 1.0
ZN T:ZN1002 3.8 0.0 1.0
C T:CYS104 3.9 0.0 1.0
ZN T:ZN1001 3.9 0.0 1.0
CB T:CYS108 3.9 0.0 1.0
CA T:CYS105 4.2 0.0 1.0
SG T:CYS122 4.3 0.0 1.0
CA T:CYS148 4.4 0.0 1.0
SG T:CYS145 4.6 0.0 1.0
N T:CYS104 4.6 0.0 1.0
O T:CYS104 4.7 0.0 1.0
CB T:CYS150 4.7 0.0 1.0
SG T:CYS153 4.8 0.0 1.0
N T:CYS108 4.9 0.0 1.0
CA T:CYS108 4.9 0.0 1.0

Zinc binding site 5 out of 7 in 5gmk

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:0.0
occ:1.00
SG T:CYS153 2.3 0.0 1.0
CB T:CYS150 2.3 0.0 1.0
SG T:CYS150 2.3 0.0 1.0
SG T:CYS122 2.3 0.0 1.0
SG T:CYS104 2.3 0.0 1.0
CB T:CYS104 3.2 0.0 1.0
CB T:CYS153 3.5 0.0 1.0
CA T:CYS150 3.8 0.0 1.0
O T:CYS122 3.8 0.0 1.0
CB T:CYS122 3.8 0.0 1.0
ZN T:ZN1000 3.9 0.0 1.0
N T:CYS153 3.9 0.0 1.0
CA T:CYS153 4.1 0.0 1.0
ZN T:ZN1002 4.1 0.0 1.0
CA T:CYS104 4.2 0.0 1.0
N T:CYS104 4.2 0.0 1.0
SG T:CYS108 4.3 0.0 1.0
C T:CYS122 4.4 0.0 1.0
CA T:CYS122 4.5 0.0 1.0
C T:CYS150 4.5 0.0 1.0
N T:CYS150 4.6 0.0 1.0
CG n:PRO68 4.6 0.7 1.0
N T:ARG151 4.9 0.0 1.0
CB T:CYS108 5.0 0.0 1.0
CB T:CYS145 5.0 0.0 1.0

Zinc binding site 6 out of 7 in 5gmk

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:0.0
occ:1.00
SG T:CYS145 2.3 0.0 1.0
SG T:CYS122 2.3 0.0 1.0
SG T:CYS108 2.3 0.0 1.0
SG T:CYS120 2.3 0.0 1.0
CB T:CYS122 2.8 0.0 1.0
CB T:CYS108 3.0 0.0 1.0
CB T:CYS120 3.2 0.0 1.0
CB T:CYS145 3.4 0.0 1.0
ZN T:ZN1000 3.8 0.0 1.0
CA T:CYS108 3.8 0.0 1.0
SG T:CYS148 3.9 0.0 1.0
ZN T:ZN1001 4.1 0.0 1.0
CA T:CYS122 4.3 0.0 1.0
SG T:CYS104 4.6 0.0 1.0
CD2 T:HIS147 4.6 0.0 1.0
CA T:CYS120 4.7 0.0 1.0
N T:CYS108 4.7 0.0 1.0
CA T:CYS145 4.8 0.0 1.0
N T:CYS122 4.8 0.0 1.0
C T:CYS108 4.9 0.0 1.0
CB T:CYS148 4.9 0.0 1.0
C T:CYS122 4.9 0.0 1.0
O T:CYS108 4.9 0.0 1.0
CB T:CYS104 5.0 0.0 1.0
CB T:CYS150 5.0 0.0 1.0

Zinc binding site 7 out of 7 in 5gmk

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:30.0
occ:1.00
SG F:CYS91 2.3 20.0 1.0
SG F:CYS54 2.3 20.0 1.0
SG F:CYS88 2.3 20.0 1.0
SG F:CYS51 2.3 20.0 1.0
CB F:CYS88 3.3 20.0 1.0
CB F:CYS51 3.4 20.0 1.0
CB F:CYS91 3.7 20.0 1.0
CB F:CYS54 3.7 20.0 1.0
N F:CYS54 3.8 8.8 1.0
N F:CYS91 4.0 10.3 1.0
CA F:CYS54 4.3 9.4 1.0
CB F:GLU56 4.3 20.0 1.0
CA F:CYS91 4.4 10.8 1.0
CB F:GLU53 4.4 20.0 1.0
CB F:ARG90 4.6 20.0 1.0
O F:CYS91 4.7 9.8 1.0
CA F:CYS88 4.7 9.4 1.0
N F:GLU56 4.8 9.3 1.0
C F:GLU53 4.8 9.1 1.0
C F:CYS54 4.8 8.7 1.0
CA F:CYS51 4.8 6.2 1.0
C F:CYS91 4.8 10.0 1.0
OE1 F:GLU53 4.8 20.0 1.0
CB F:ASN93 4.9 20.0 1.0
N F:GLU53 4.9 7.8 1.0
N F:ARG90 4.9 9.3 1.0
N F:ASN55 5.0 8.2 1.0
CA F:GLU53 5.0 8.1 1.0
C F:ARG90 5.0 11.6 1.0

Reference:

R.Wan, C.Yan, R.Bai, G.Huang, Y.Shi. Structure of A Yeast Catalytic Step I Spliceosome at 3.4 Angstrom Resolution Science V. 353 895 2016.
ISSN: ESSN 1095-9203
PubMed: 27445308
DOI: 10.1126/SCIENCE.AAG2235
Page generated: Wed Dec 16 06:19:39 2020

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