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Zinc in PDB 9esh: Structure of A B-State Intermediate Committed to Discard (Bd-I State)

Enzymatic activity of Structure of A B-State Intermediate Committed to Discard (Bd-I State)

All present enzymatic activity of Structure of A B-State Intermediate Committed to Discard (Bd-I State):
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 9esh:

The structure of Structure of A B-State Intermediate Committed to Discard (Bd-I State) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A B-State Intermediate Committed to Discard (Bd-I State) (pdb code 9esh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A B-State Intermediate Committed to Discard (Bd-I State), PDB code: 9esh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9esh

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Zinc binding site 1 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-I State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A B-State Intermediate Committed to Discard (Bd-I State) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:133.8
occ:1.00
 SG M:CYS23 2.3 107.9 1.0
SG M:CYS80 2.3 107.8 1.0
SG M:CYS83 2.3 116.0 1.0
SG M:CYS26 2.3 105.3 1.0
CB M:CYS80 3.1 107.8 1.0
CB M:CYS83 3.3 116.0 1.0
CB M:CYS23 3.7 107.9 1.0
OG M:SER82 3.7 104.3 1.0
N M:CYS23 3.8 107.9 1.0
CB M:CYS26 3.8 105.3 1.0
N M:CYS83 3.8 116.0 1.0
O M:CYS23 4.1 107.9 1.0
CA M:CYS23 4.2 107.9 1.0
CA M:CYS83 4.2 116.0 1.0
CG2 M:ILE22 4.3 94.4 1.0
N M:CYS26 4.4 105.3 1.0
C M:CYS23 4.5 107.9 1.0
CA M:CYS80 4.5 107.8 1.0
CA M:CYS26 4.7 105.3 1.0
C M:ILE22 4.8 94.4 1.0
C M:CYS83 4.9 116.0 1.0
CB M:SER82 5.0 104.3 1.0
C M:SER82 5.0 104.3 1.0
C M:CYS80 5.0 107.8 1.0

Zinc binding site 2 out of 6 in 9esh

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Zinc binding site 2 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-I State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A B-State Intermediate Committed to Discard (Bd-I State) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn402

b:166.5
occ:1.00
 SG M:CYS70 2.3 103.9 1.0
SG M:CYS47 2.3 115.7 1.0
SG M:CYS44 2.4 99.0 1.0
SG M:CYS73 2.4 117.7 1.0
CB M:CYS47 2.9 115.7 1.0
CB M:CYS73 3.2 117.7 1.0
N M:CYS47 3.5 115.7 1.0
NE2 M:GLN121 3.5 194.1 1.0
CB M:CYS70 3.5 103.9 1.0
N M:CYS73 3.6 117.7 1.0
CA M:CYS47 3.7 115.7 1.0
CB M:CYS44 3.8 99.0 1.0
N M:CYS70 4.0 103.9 1.0
CA M:CYS73 4.0 117.7 1.0
CG2 M:ILE69 4.0 90.8 1.0
CA M:CYS70 4.3 103.9 1.0
CB M:ILE46 4.5 116.0 1.0
C M:ILE46 4.6 116.0 1.0
C M:GLY72 4.6 116.8 1.0
C M:CYS70 4.7 103.9 1.0
CD M:GLN121 4.8 194.1 1.0
CG2 M:ILE46 4.8 116.0 1.0
O M:CYS70 4.9 103.9 1.0
CA M:ILE46 5.0 116.0 1.0
CA M:GLY72 5.0 116.8 1.0

Zinc binding site 3 out of 6 in 9esh

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Zinc binding site 3 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-I State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A B-State Intermediate Committed to Discard (Bd-I State) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn201

b:62.3
occ:1.00
 SG O:CYS101 2.3 51.4 1.0
SG O:CYS137 2.3 52.9 1.0
SG O:CYS105 2.3 53.5 1.0
SG O:CYS102 2.3 48.9 1.0
CB O:CYS105 3.2 53.5 1.0
CB O:CYS102 3.5 48.9 1.0
N O:CYS102 3.5 48.9 1.0
CB O:CYS137 3.6 52.9 1.0
CB O:CYS101 3.7 51.4 1.0
ZN O:ZN202 3.9 74.0 1.0
ZN O:ZN203 3.9 74.3 1.0
CA O:CYS102 4.0 48.9 1.0
N O:CYS105 4.2 53.5 1.0
CA O:CYS105 4.3 53.5 1.0
C O:CYS101 4.3 51.4 1.0
CB O:HIS136 4.4 52.5 1.0
C O:CYS102 4.4 48.9 1.0
O O:CYS102 4.5 48.9 1.0
N O:CYS137 4.5 52.9 1.0
CA O:CYS101 4.6 51.4 1.0
CB O:CYS139 4.7 64.8 1.0
SG O:CYS119 4.7 59.8 1.0
SG O:CYS134 4.7 62.4 1.0
CA O:CYS137 4.7 52.9 1.0

Zinc binding site 4 out of 6 in 9esh

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Zinc binding site 4 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-I State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A B-State Intermediate Committed to Discard (Bd-I State) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn202

b:74.0
occ:1.00
 SG O:CYS142 2.3 62.3 1.0
SG O:CYS119 2.3 59.8 1.0
SG O:CYS101 2.3 51.4 1.0
SG O:CYS139 2.3 64.8 1.0
CB O:CYS139 2.7 64.8 1.0
CB O:CYS101 2.8 51.4 1.0
CB O:CYS119 2.9 59.8 1.0
CB O:CYS142 3.8 62.3 1.0
ZN O:ZN203 3.8 74.3 1.0
ZN O:ZN201 3.9 62.3 1.0
CA O:CYS101 4.1 51.4 1.0
N O:CYS101 4.1 51.4 1.0
CA O:CYS139 4.2 64.8 1.0
CA O:CYS119 4.3 59.8 1.0
CB O:CYS105 4.4 53.5 1.0
SG O:CYS105 4.4 53.5 1.0
SG O:CYS137 4.4 52.9 1.0
N O:CYS142 4.4 62.3 1.0
CA O:CYS142 4.5 62.3 1.0
C O:CYS119 4.6 59.8 1.0
C O:CYS139 4.9 64.8 1.0
O O:CYS119 4.9 59.8 1.0
N O:CYS102 4.9 48.9 1.0

Zinc binding site 5 out of 6 in 9esh

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Zinc binding site 5 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-I State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A B-State Intermediate Committed to Discard (Bd-I State) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn203

b:74.3
occ:1.00
 SG O:CYS134 2.3 62.4 1.0
SG O:CYS117 2.3 56.7 1.0
SG O:CYS105 2.3 53.5 1.0
SG O:CYS119 2.4 59.8 1.0
CB O:CYS117 2.8 56.7 1.0
CB O:CYS105 3.1 53.5 1.0
CB O:CYS119 3.6 59.8 1.0
CB O:CYS134 3.8 62.4 1.0
ZN O:ZN202 3.8 74.0 1.0
ZN O:ZN201 3.9 62.3 1.0
N O:CYS119 4.2 59.8 1.0
CA O:CYS105 4.2 53.5 1.0
CA O:CYS117 4.2 56.7 1.0
CD2 O:HIS136 4.4 52.5 1.0
SG O:CYS101 4.5 51.4 1.0
CA O:CYS119 4.6 59.8 1.0
CB O:HIS136 4.6 52.5 1.0
CB O:CYS139 4.6 64.8 1.0
N O:ILE118 4.6 57.6 1.0
SG O:CYS137 4.7 52.9 1.0
C O:CYS117 4.7 56.7 1.0
CG O:HIS136 4.9 52.5 1.0
O O:CYS105 4.9 53.5 1.0
CA O:CYS134 4.9 62.4 1.0

Zinc binding site 6 out of 6 in 9esh

Go back to Zinc Binding Sites List in 9esh
Zinc binding site 6 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-I State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A B-State Intermediate Committed to Discard (Bd-I State) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn401

b:279.9
occ:1.00
 NE2 P:HIS135 2.1 216.8 1.0
SG P:CYS131 2.3 221.5 1.0
SG P:CYS125 2.3 233.6 1.0
SG P:CYS117 2.3 209.9 1.0
CB P:CYS131 2.6 221.5 1.0
CE1 P:HIS135 2.7 216.8 1.0
CD2 P:HIS135 2.9 216.8 1.0
CB P:CYS117 3.4 209.9 1.0
ND1 P:HIS135 3.6 216.8 1.0
CG P:HIS135 3.7 216.8 1.0
O P:TYR133 3.9 207.4 1.0
CB P:CYS125 3.9 233.6 1.0
CA P:CYS131 4.1 221.5 1.0
O P:GLY128 4.4 229.3 1.0
C P:TYR133 4.6 207.4 1.0
N P:TYR133 4.6 207.4 1.0
CA P:CYS117 4.7 209.9 1.0
CB P:TYR133 4.7 207.4 1.0
C P:CYS131 4.7 221.5 1.0
CA P:TYR133 4.9 207.4 1.0
N P:GLU132 4.9 213.5 1.0
N P:CYS131 4.9 221.5 1.0

Reference:

K.Soni, K.Wild, I.M.Sinning. Structures of Aberrant Spliceosome Intermediates on Their Way to Disassembly To Be Published.
Page generated: Sun Feb 9 01:05:12 2025

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