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Magnesium in PDB 1s0v: Structural Basis For Substrate Selection By T7 Rna Polymerase

Enzymatic activity of Structural Basis For Substrate Selection By T7 Rna Polymerase

All present enzymatic activity of Structural Basis For Substrate Selection By T7 Rna Polymerase:
2.7.7.6;

Protein crystallography data

The structure of Structural Basis For Substrate Selection By T7 Rna Polymerase, PDB code: 1s0v was solved by D.Temiakov, V.Patlan, M.Anikin, W.T.Mcallister, S.Yokoyama, D.G.Vassylyev, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 81.133, 87.703, 206.531, 91.93, 91.02, 110.66
R / Rfree (%) 25.5 / 30.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis For Substrate Selection By T7 Rna Polymerase (pdb code 1s0v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structural Basis For Substrate Selection By T7 Rna Polymerase, PDB code: 1s0v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1s0v

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Magnesium binding site 1 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3005

b:18.4
occ:1.00
 O A:HOH3015 2.2 47.1 1.0
O2' A:APC2000 2.2 61.1 1.0
OH A:TYR639 2.4 9.3 1.0
O4 F:U8 2.8 16.0 1.0
C2' A:APC2000 3.0 61.5 1.0
C4 F:U8 3.1 14.2 1.0
N3 F:U8 3.2 12.5 1.0
CZ A:TYR639 3.6 6.6 1.0
C2 F:U8 3.9 13.8 1.0
C5 F:U8 4.0 13.0 1.0
CE2 A:TYR639 4.0 6.1 1.0
C1' A:APC2000 4.1 66.1 1.0
C3' A:APC2000 4.2 60.4 1.0
O2 F:U8 4.4 16.3 1.0
CE A:MET635 4.4 56.4 1.0
N9 A:APC2000 4.4 71.0 1.0
O3' A:APC2000 4.5 58.3 1.0
N1 F:U8 4.5 18.5 1.0
N6 E:DA11 4.5 7.8 1.0
C6 F:U8 4.6 16.7 1.0
N1 E:DA11 4.6 5.3 1.0
C2' F:U8 4.7 23.9 1.0
CE1 A:TYR639 4.7 5.6 1.0
C4 A:APC2000 4.8 75.0 1.0
O2' F:U8 4.8 23.6 1.0
C6 E:DA11 4.8 6.0 1.0
N3 A:APC2000 4.8 77.2 1.0
O A:MET635 4.9 43.9 1.0

Magnesium binding site 2 out of 8 in 1s0v

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Magnesium binding site 2 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:22.6
occ:1.00
 O A:HOH3217 2.1 88.8 1.0
O1G A:APC2000 2.1 37.9 1.0
O2B A:APC2000 2.3 42.7 1.0
O A:HOH3172 2.6 76.8 1.0
PG A:APC2000 3.1 36.5 1.0
PB A:APC2000 3.4 39.7 1.0
O3G A:APC2000 3.5 34.4 1.0
O3B A:APC2000 3.5 38.6 1.0
O A:HOH3182 3.6 50.4 1.0
O1A A:APC2000 3.6 45.3 1.0
OD2 A:ASP471 3.8 64.6 1.0
CE A:LYS472 3.9 61.1 1.0
C3A A:APC2000 4.3 43.4 1.0
PA A:APC2000 4.4 44.3 1.0
O2G A:APC2000 4.4 39.2 1.0
NZ A:LYS472 4.5 58.6 1.0
O1B A:APC2000 4.7 40.8 1.0
CG A:ASP471 4.7 62.0 1.0
OD1 A:ASP471 4.8 61.6 1.0

Magnesium binding site 3 out of 8 in 1s0v

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Magnesium binding site 3 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:65.1
occ:1.00
 O2B B:APC2001 2.4 59.4 1.0
O1G B:APC2001 2.5 63.3 1.0
O3G B:APC2001 2.7 68.0 1.0
PG B:APC2001 3.0 61.0 1.0
OD2 B:ASP471 3.3 52.4 1.0
PB B:APC2001 3.6 56.6 1.0
O3B B:APC2001 3.7 60.4 1.0
O1A B:APC2001 3.9 50.6 1.0
OD1 B:ASP471 3.9 52.9 1.0
CG B:ASP471 4.0 52.5 1.0
NZ B:LYS472 4.2 68.6 1.0
O2G B:APC2001 4.4 66.9 1.0
O1B B:APC2001 4.6 59.2 1.0
CE B:LYS472 4.7 66.1 1.0
C3A B:APC2001 4.8 53.4 1.0
CD B:LYS472 4.9 64.1 1.0

Magnesium binding site 4 out of 8 in 1s0v

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Magnesium binding site 4 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3006

b:34.4
occ:1.00
 O2' B:APC2001 2.1 28.1 1.0
OH B:TYR639 2.5 23.0 1.0
O B:HOH3164 2.6 75.2 1.0
C2' B:APC2001 2.7 33.8 1.0
O3' B:APC2001 3.2 32.5 1.0
C3' B:APC2001 3.5 34.0 1.0
CZ B:TYR639 3.8 23.8 1.0
N3 I:U8 3.9 6.8 1.0
C4 I:U8 4.0 7.7 1.0
C2 I:U8 4.0 8.1 1.0
C5 I:U8 4.1 8.4 1.0
N1 I:U8 4.1 8.2 1.0
C1' B:APC2001 4.1 37.8 1.0
C6 I:U8 4.1 8.7 1.0
O B:HOH3084 4.2 24.7 1.0
O4 I:U8 4.3 9.1 1.0
C2' I:U8 4.4 19.0 1.0
C3' I:U8 4.5 22.7 1.0
CE2 B:TYR639 4.5 23.0 1.0
O B:HOH3093 4.5 5.9 1.0
O2 I:U8 4.5 9.8 1.0
N1 H:DA11 4.7 19.6 1.0
CE1 B:TYR639 4.9 21.2 1.0
C4' B:APC2001 4.9 36.6 1.0
C1' I:U8 4.9 13.0 1.0
CE B:MET635 4.9 8.5 1.0

Magnesium binding site 5 out of 8 in 1s0v

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Magnesium binding site 5 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3003

b:41.7
occ:1.00
 O1G C:APC2002 2.3 76.2 1.0
O3G C:APC2002 2.3 78.3 1.0
O2B C:APC2002 2.4 70.2 1.0
PG C:APC2002 2.7 72.6 1.0
O C:HOH3136 3.0 58.0 1.0
O1A C:APC2002 3.0 68.6 1.0
PB C:APC2002 3.5 68.3 1.0
O3B C:APC2002 3.5 72.5 1.0
OD2 C:ASP471 4.0 92.5 1.0
O2G C:APC2002 4.1 78.3 1.0
PA C:APC2002 4.3 65.8 1.0
C3A C:APC2002 4.3 68.4 1.0
OD1 C:ASP471 4.5 91.8 1.0
O C:HOH3141 4.6 48.7 1.0
CG C:ASP471 4.6 92.9 1.0
O1B C:APC2002 4.8 71.6 1.0
NZ C:LYS631 5.0 72.0 1.0

Magnesium binding site 6 out of 8 in 1s0v

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Magnesium binding site 6 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3007

b:46.3
occ:1.00
 O2' C:APC2002 2.4 67.7 1.0
OH C:TYR639 2.5 66.5 1.0
C2' C:APC2002 2.8 69.8 1.0
O C:HOH3009 3.3 28.7 1.0
CZ C:TYR639 3.4 65.9 1.0
CE2 C:TYR639 3.7 65.9 1.0
C1' C:APC2002 3.7 70.6 1.0
O C:HOH3022 3.7 11.3 1.0
O C:MET635 3.8 76.3 1.0
N9 C:APC2002 3.9 74.3 1.0
N3 L:U8 4.0 48.1 1.0
O4 L:U8 4.0 41.7 1.0
C3' C:APC2002 4.1 70.2 1.0
C4 L:U8 4.3 46.4 1.0
C2 L:U8 4.3 49.9 1.0
C8 C:APC2002 4.4 74.2 1.0
C4 C:APC2002 4.5 75.3 1.0
O3' C:APC2002 4.5 67.2 1.0
C2' L:U8 4.6 47.5 1.0
O2 L:U8 4.6 51.9 1.0
CE1 C:TYR639 4.6 65.7 1.0
CE C:MET635 4.7 80.8 1.0
N1 L:U8 4.8 49.2 1.0
N3 C:APC2002 4.8 76.5 1.0
C5 L:U8 4.9 47.7 1.0
C C:MET635 5.0 76.7 1.0

Magnesium binding site 7 out of 8 in 1s0v

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Magnesium binding site 7 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3004

b:79.5
occ:1.00
 O2B D:APC2003 2.3 57.8 1.0
O1G D:APC2003 2.6 58.3 1.0
PG D:APC2003 3.2 57.2 1.0
O3G D:APC2003 3.2 63.3 1.0
OD2 D:ASP471 3.4 0.2 1.0
O3B D:APC2003 3.4 59.6 1.0
PB D:APC2003 3.5 56.4 1.0
O1A D:APC2003 3.5 55.5 1.0
O D:HOH3137 3.8 87.1 1.0
NZ D:LYS472 3.9 0.8 1.0
CG D:ASP471 4.3 0.5 1.0
O D:HOH3045 4.3 48.8 1.0
OD1 D:ASP471 4.4 0.1 1.0
C3A D:APC2003 4.4 56.9 1.0
PA D:APC2003 4.5 55.8 1.0
CE D:LYS472 4.7 0.4 1.0
O2G D:APC2003 4.7 58.6 1.0
O1B D:APC2003 4.7 61.6 1.0

Magnesium binding site 8 out of 8 in 1s0v

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Magnesium binding site 8 out of 8 in the Structural Basis For Substrate Selection By T7 Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Basis For Substrate Selection By T7 Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3008

b:16.6
occ:1.00
 O2' D:APC2003 2.2 49.4 1.0
OH D:TYR639 2.7 76.0 1.0
C2' D:APC2003 3.5 51.9 1.0
N3 O:U8 3.6 42.7 1.0
C4 O:U8 3.6 41.5 1.0
O4 O:U8 3.8 38.6 1.0
CZ D:TYR639 3.9 72.9 1.0
C2 O:U8 3.9 43.2 1.0
C5 O:U8 4.0 42.5 1.0
N1 O:U8 4.2 44.8 1.0
C6 O:U8 4.2 43.8 1.0
CE2 D:TYR639 4.3 72.0 1.0
C1' D:APC2003 4.4 54.3 1.0
O2 O:U8 4.5 42.2 1.0
C2' O:U8 4.5 52.0 1.0
N3 D:APC2003 4.6 60.1 1.0
N1 N:DA11 4.6 52.6 1.0
C3' D:APC2003 4.7 51.4 1.0
N6 N:DA11 4.8 51.8 1.0
O3' D:APC2003 4.8 48.2 1.0
O2' O:U8 4.8 50.2 1.0
N9 D:APC2003 4.9 57.0 1.0
C4 D:APC2003 5.0 59.0 1.0

Reference:

D.Temiakov, V.Patlan, M.Anikin, W.T.Mcallister, S.Yokoyama, D.G.Vassylyev. Structural Basis For Substrate Selection By T7 Rna Polymerase. Cell(Cambridge,Mass.) V. 116 381 2004.
ISSN: ISSN 0092-8674
PubMed: 15016373
DOI: 10.1016/S0092-8674(04)00059-5
Page generated: Tue Aug 13 13:12:30 2024

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