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Magnesium in PDB 9fpy: Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3

Enzymatic activity of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3

All present enzymatic activity of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3:
2.7.7.6; 3.6.1.15;

Other elements in 9fpy:

The structure of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3 (pdb code 9fpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3, PDB code: 9fpy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9fpy

Go back to Magnesium Binding Sites List in 9fpy
Magnesium binding site 1 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg101

b:101.7
occ:1.00
 OP1 U:G9 1.9 112.3 1.0
P U:G9 3.1 107.1 1.0
OP1 U:U8 3.1 116.0 1.0
OP2 U:G9 3.6 105.8 1.0
O5' U:G9 3.7 94.2 1.0
OP2 U:U11 4.0 99.1 1.0
H5'' U:U8 4.0 118.1 1.0
OP1 U:U11 4.4 80.0 1.0
O3' U:U8 4.4 100.0 1.0
P U:U8 4.5 128.4 1.0
P U:U11 4.7 93.1 1.0
OP2 U:G10 4.8 88.7 1.0
C5' U:U8 4.9 118.7 1.0
O5' U:U8 4.9 120.8 1.0

Magnesium binding site 2 out of 4 in 9fpy

Go back to Magnesium Binding Sites List in 9fpy
Magnesium binding site 2 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg102

b:85.3
occ:1.00
 OP1 U:A58 3.5 111.2 1.0
O4 U:U47 3.9 90.8 1.0
O4 U:U59 4.2 111.0 1.0
N7 U:A58 4.3 98.2 1.0
H4' U:1MA57 4.5 129.9 0.0
O4' U:A21 4.5 70.9 1.0
H8 U:A58 4.5 98.1 1.0
OP2 U:A21 4.7 72.0 1.0
OP1 U:U19 4.8 86.4 0.5
C8 U:A58 4.8 98.5 1.0
H62 U:A58 4.9 91.6 1.0
C4 U:U47 5.0 88.2 1.0
H2 U:A15 5.0 82.6 1.0
H1' U:A21 5.0 73.7 1.0

Magnesium binding site 3 out of 4 in 9fpy

Go back to Magnesium Binding Sites List in 9fpy
Magnesium binding site 3 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:63.0
occ:1.00
 OD1 A:ASP417 1.9 71.4 1.0
OD1 A:ASP415 2.3 70.0 1.0
OD1 A:ASP419 2.4 68.7 1.0
CG A:ASP417 2.7 64.2 1.0
OD2 A:ASP417 2.9 65.1 1.0
CG A:ASP415 3.2 70.8 1.0
CG A:ASP419 3.3 70.5 1.0
OD2 A:ASP415 3.4 76.0 1.0
OD2 A:ASP419 3.4 68.8 1.0
H A:ASP417 3.8 60.6 1.0
H S:ASN226 4.1 29.0 1.0
HB2 S:ASN226 4.1 25.2 1.0
CB A:ASP417 4.1 52.7 1.0
O A:ASP415 4.2 63.5 1.0
O S:ASN226 4.3 30.8 1.0
H A:ASP415 4.3 63.1 1.0
HB3 A:ASP417 4.5 58.4 1.0
N A:ASP417 4.5 58.5 1.0
CB A:ASP415 4.6 63.7 1.0
H A:ASP419 4.6 60.9 1.0
C A:ASP417 4.6 58.0 1.0
CA A:ASP417 4.6 53.3 1.0
HB2 A:ASP417 4.7 54.9 1.0
C A:ASP415 4.7 57.7 1.0
CB A:ASP419 4.7 63.2 1.0
N A:ASP419 4.8 59.5 1.0
O A:ASP417 4.8 58.9 1.0
N A:GLY418 4.9 60.1 1.0
HB2 A:ASP415 4.9 65.1 1.0
N S:ASN226 4.9 31.9 1.0
N A:ASP415 4.9 63.0 1.0
CA A:ASP415 5.0 58.9 1.0
H A:GLY418 5.0 59.6 1.0
CB S:ASN226 5.0 23.9 1.0

Magnesium binding site 4 out of 4 in 9fpy

Go back to Magnesium Binding Sites List in 9fpy
Magnesium binding site 4 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex Assembly Intermediate 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg701

b:76.5
occ:1.00
 O2' U:U35 1.8 73.9 1.0
HD3 Y:ARG120 2.1 102.0 1.0
CZ Y:ARG120 2.2 100.8 1.0
NH1 Y:ARG120 2.2 96.3 1.0
HH11 Y:ARG120 2.3 97.6 1.0
NE Y:ARG120 2.3 101.5 1.0
CD Y:ARG120 2.6 103.1 1.0
HH12 Y:ARG120 2.8 98.7 1.0
HE Y:ARG120 2.8 100.1 1.0
HD2 Y:ARG120 2.9 101.1 1.0
NH2 Y:ARG120 3.0 103.3 1.0
C2' U:U35 3.2 71.3 1.0
HH22 Y:ARG120 3.5 101.0 1.0
HH21 Y:ARG120 3.5 103.1 1.0
H2' U:U35 3.7 68.3 1.0
O3' U:U35 3.7 82.6 1.0
C3' U:U35 4.0 75.6 1.0
H1' U:U35 4.0 65.8 1.0
CG Y:ARG120 4.0 97.8 1.0
HG3 Y:ARG120 4.1 98.2 1.0
OD1 Y:ASN121 4.2 112.6 1.0
C1' U:U35 4.2 66.7 1.0
H3' U:U35 4.2 73.0 1.0
HG2 Y:ARG120 4.4 99.4 1.0
O2 U:U35 4.5 58.9 1.0
HD2 Y:PHE124 4.5 89.1 1.0
OP2 U:G36 4.7 80.3 1.0
CD2 Y:PHE124 4.7 87.7 1.0
N1 U:U35 4.8 64.8 1.0
HB3 Y:ARG120 4.8 95.5 1.0
P U:G36 4.8 92.3 1.0
HA Y:ASN121 4.8 100.7 1.0
HG Y:SER163 4.9 83.7 1.0
C2 U:U35 4.9 61.2 1.0
HE2 Y:PHE124 4.9 83.7 1.0
CE2 Y:PHE124 4.9 79.6 1.0

Reference:

C.Grimm, J.Bartuli, U.Fischer. Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex at 2.65A Resolution To Be Published.
Page generated: Sat Aug 16 02:07:56 2025

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