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

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

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

Other elements in 9esi:

The structure of Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) (pdb code 9esi). 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-II State), PDB code: 9esi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9esi

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Zinc binding site 1 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:101.8
occ:1.00
 SG M:CYS23 2.3 74.1 1.0
SG M:CYS80 2.3 76.4 1.0
SG M:CYS83 2.3 79.3 1.0
SG M:CYS26 2.3 73.9 1.0
OG M:SER82 3.1 71.6 1.0
CB M:CYS80 3.2 76.4 1.0
CB M:CYS83 3.4 79.3 1.0
CB M:CYS26 3.5 73.9 1.0
CB M:CYS23 3.6 74.1 1.0
N M:CYS83 3.6 79.3 1.0
N M:CYS23 3.7 74.1 1.0
O M:CYS23 4.0 74.1 1.0
CA M:CYS23 4.1 74.1 1.0
CA M:CYS83 4.1 79.3 1.0
CB M:SER82 4.4 71.6 1.0
N M:CYS26 4.4 73.9 1.0
CG2 M:ILE22 4.4 63.5 1.0
C M:CYS23 4.4 74.1 1.0
CA M:CYS26 4.5 73.9 1.0
CA M:CYS80 4.6 76.4 1.0
C M:SER82 4.7 71.6 1.0
N M:SER82 4.8 71.6 1.0
C M:ILE22 4.8 63.5 1.0
CA M:SER82 4.9 71.6 1.0
C M:CYS83 4.9 79.3 1.0
C M:CYS80 4.9 76.4 1.0

Zinc binding site 2 out of 6 in 9esi

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Zinc binding site 2 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn402

b:170.9
occ:1.00
 SG M:CYS70 2.3 87.7 1.0
SG M:CYS73 2.3 100.6 1.0
SG M:CYS47 2.3 103.5 1.0
SG M:CYS44 2.3 93.6 1.0
CB M:CYS47 2.8 103.5 1.0
N M:CYS47 3.4 103.5 1.0
CB M:CYS73 3.4 100.6 1.0
CB M:CYS44 3.4 93.6 1.0
CB M:CYS70 3.6 87.7 1.0
N M:CYS73 3.6 100.6 1.0
CA M:CYS47 3.7 103.5 1.0
NE2 M:GLN121 3.7 208.8 1.0
N M:CYS70 4.0 87.7 1.0
CA M:CYS73 4.1 100.6 1.0
CA M:CYS70 4.3 87.7 1.0
C M:ILE46 4.5 98.9 1.0
CB M:ILE46 4.6 98.9 1.0
C M:GLY72 4.6 104.4 1.0
C M:CYS70 4.8 87.7 1.0
CA M:CYS44 4.8 93.6 1.0
O M:CYS70 4.9 87.7 1.0
CA M:ILE46 4.9 98.9 1.0
CA M:GLY72 4.9 104.4 1.0
C M:CYS47 4.9 103.5 1.0
N M:ILE46 4.9 98.9 1.0

Zinc binding site 3 out of 6 in 9esi

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Zinc binding site 3 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn201

b:71.8
occ:1.00
 SG O:CYS101 2.3 47.4 1.0
SG O:CYS137 2.3 49.7 1.0
SG O:CYS105 2.3 48.4 1.0
SG O:CYS102 2.3 44.7 1.0
CB O:CYS105 3.1 48.4 1.0
CB O:CYS102 3.5 44.7 1.0
N O:CYS102 3.6 44.7 1.0
CB O:CYS137 3.6 49.7 1.0
CB O:CYS101 3.6 47.4 1.0
ZN O:ZN202 3.8 80.1 1.0
ZN O:ZN203 3.9 75.8 1.0
CA O:CYS102 4.0 44.7 1.0
N O:CYS105 4.2 48.4 1.0
C O:CYS101 4.2 47.4 1.0
CA O:CYS105 4.3 48.4 1.0
O O:CYS102 4.4 44.7 1.0
C O:CYS102 4.4 44.7 1.0
CB O:HIS136 4.4 48.9 1.0
SG O:CYS134 4.4 60.1 1.0
N O:CYS137 4.5 49.7 1.0
CA O:CYS101 4.5 47.4 1.0
CB O:CYS139 4.6 60.6 1.0
CA O:CYS137 4.7 49.7 1.0
SG O:CYS119 4.7 58.7 1.0

Zinc binding site 4 out of 6 in 9esi

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Zinc binding site 4 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn202

b:80.1
occ:1.00
 SG O:CYS142 2.3 54.4 1.0
SG O:CYS139 2.3 60.6 1.0
SG O:CYS101 2.3 47.4 1.0
SG O:CYS119 2.3 58.7 1.0
CB O:CYS139 2.6 60.6 1.0
CB O:CYS101 3.0 47.4 1.0
CB O:CYS119 3.1 58.7 1.0
CB O:CYS142 3.8 54.4 1.0
ZN O:ZN203 3.8 75.8 1.0
ZN O:ZN201 3.8 71.8 1.0
CA O:CYS139 4.1 60.6 1.0
SG O:CYS105 4.2 48.4 1.0
CA O:CYS101 4.3 47.4 1.0
SG O:CYS137 4.3 49.7 1.0
CB O:CYS105 4.3 48.4 1.0
N O:CYS142 4.3 54.4 1.0
N O:CYS101 4.4 47.4 1.0
CA O:CYS119 4.4 58.7 1.0
CA O:CYS142 4.5 54.4 1.0
C O:CYS139 4.7 60.6 1.0
C O:CYS119 4.7 58.7 1.0
CB O:CYS134 4.8 60.1 1.0
N O:CYS139 4.9 60.6 1.0
SG O:CYS134 5.0 60.1 1.0
O O:CYS119 5.0 58.7 1.0

Zinc binding site 5 out of 6 in 9esi

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Zinc binding site 5 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn203

b:75.8
occ:1.00
 SG O:CYS134 2.3 60.1 1.0
SG O:CYS117 2.3 54.9 1.0
SG O:CYS105 2.3 48.4 1.0
SG O:CYS119 2.3 58.7 1.0
CB O:CYS117 2.8 54.9 1.0
CB O:CYS134 3.2 60.1 1.0
CB O:CYS105 3.2 48.4 1.0
CB O:CYS119 3.8 58.7 1.0
ZN O:ZN202 3.8 80.1 1.0
ZN O:ZN201 3.9 71.8 1.0
N O:CYS119 4.2 58.7 1.0
CA O:CYS105 4.2 48.4 1.0
CA O:CYS117 4.3 54.9 1.0
CA O:CYS134 4.4 60.1 1.0
CD2 O:HIS136 4.5 48.9 1.0
SG O:CYS101 4.5 47.4 1.0
N O:ILE118 4.6 54.7 1.0
CB O:HIS136 4.6 48.9 1.0
CA O:CYS119 4.6 58.7 1.0
C O:CYS117 4.6 54.9 1.0
SG O:CYS137 4.7 49.7 1.0
CB O:CYS139 4.7 60.6 1.0
CG O:HIS136 4.9 48.9 1.0
O O:CYS105 5.0 48.4 1.0

Zinc binding site 6 out of 6 in 9esi

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Zinc binding site 6 out of 6 in the Structure of A B-State Intermediate Committed to Discard (Bd-II 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-II State) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn401

b:272.3
occ:1.00
 NE2 P:HIS135 2.1 172.3 1.0
SG P:CYS117 2.3 160.8 1.0
SG P:CYS131 2.3 183.4 1.0
SG P:CYS125 2.3 179.3 1.0
CB P:CYS131 2.7 183.4 1.0
CD2 P:HIS135 2.7 172.3 1.0
CE1 P:HIS135 2.9 172.3 1.0
CB P:CYS117 3.5 160.8 1.0
OE2 P:GLU127 3.5 188.1 1.0
CG P:HIS135 3.7 172.3 1.0
ND1 P:HIS135 3.7 172.3 1.0
O P:TYR133 3.7 161.9 1.0
CB P:CYS125 3.9 179.3 1.0
CA P:CYS131 4.2 183.4 1.0
CD P:GLU127 4.3 188.1 1.0
O P:GLY128 4.4 189.0 1.0
C P:TYR133 4.5 161.9 1.0
CG P:GLU127 4.5 188.1 1.0
N P:TYR133 4.6 161.9 1.0
CB P:TYR133 4.6 161.9 1.0
CA P:CYS117 4.7 160.8 1.0
C P:CYS131 4.8 183.4 1.0
CA P:TYR133 4.8 161.9 1.0
N P:GLU132 4.9 172.3 1.0
CB P:HIS135 5.0 172.3 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 01:05:13 2025

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