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Magnesium in PDB 6ozw: Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans

Enzymatic activity of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans

All present enzymatic activity of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans:
5.6.2.2;

Protein crystallography data

The structure of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans, PDB code: 6ozw was solved by J.A.Jones, K.E.Hevener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.18 / 2.06
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.581, 98.366, 72.706, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans (pdb code 6ozw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans, PDB code: 6ozw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6ozw

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Magnesium binding site 1 out of 6 in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:38.5
occ:1.00
 O A:HOH968 1.8 33.1 1.0
O A:HOH789 2.8 24.8 1.0
NE A:ARG157 3.2 26.0 1.0
CD A:ARG157 3.5 25.6 1.0
O A:HOH811 3.7 36.4 1.0
O A:HOH866 3.8 32.7 1.0
CB A:ARG103 4.0 21.4 1.0
CG A:GLN154 4.1 18.1 1.0
CA A:GLN154 4.1 17.7 1.0
CB A:ARG157 4.2 21.5 1.0
CD A:ARG103 4.2 24.9 1.0
CZ A:ARG157 4.3 28.9 1.0
CB A:GLN154 4.5 20.5 1.0
CG A:ARG157 4.5 22.3 1.0
OG A:SER489 4.5 33.4 1.0
O A:ALA153 4.6 21.0 1.0
NH2 A:ARG157 4.6 23.9 1.0
CG A:ARG103 4.7 25.3 1.0
O A:GLN154 4.8 18.9 1.0
N A:GLN154 4.8 18.5 1.0
NH1 A:ARG103 5.0 22.2 1.0

Magnesium binding site 2 out of 6 in 6ozw

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Magnesium binding site 2 out of 6 in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:38.5
occ:1.00
 NE A:ARG158 2.7 40.0 1.0
O A:HOH864 2.9 27.2 1.0
O A:ARG158 3.0 22.0 1.0
CZ A:ARG158 3.4 37.4 1.0
CD A:ARG158 3.4 31.4 1.0
NH2 A:ARG158 3.5 43.6 1.0
CG A:ARG158 3.6 29.8 1.0
N A:ARG162 3.6 21.5 1.0
CB A:ARG162 3.8 20.3 1.0
C A:ARG158 3.9 19.1 1.0
CA A:ARG162 3.9 18.6 1.0
CA A:ARG158 4.0 20.3 1.0
O A:HOH743 4.0 24.3 1.0
CB A:ASP161 4.0 22.1 1.0
O A:HOH771 4.1 41.1 1.0
C A:ASP161 4.2 20.0 1.0
CD1 A:LEU55 4.3 25.3 1.0
CB A:ARG158 4.4 23.3 1.0
NH1 A:ARG158 4.4 41.7 1.0
CA A:ASP161 4.6 18.4 1.0
NE A:ARG162 4.7 26.1 1.0
O A:ASP161 4.8 20.5 1.0

Magnesium binding site 3 out of 6 in 6ozw

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Magnesium binding site 3 out of 6 in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:21.9
occ:1.00
 O A:HOH833 2.7 26.6 1.0
O A:HOH880 2.9 18.7 1.0
NE A:ARG318 3.1 33.2 1.0
NH2 A:ARG318 3.2 36.1 1.0
O A:HOH1005 3.4 24.9 1.0
CZ A:ARG318 3.6 38.5 1.0
CG A:MET293 3.8 17.0 1.0
CB A:ALA492 3.9 20.0 1.0
CD A:PRO493 4.0 19.7 1.0
CB A:MET293 4.2 19.2 1.0
CD A:ARG318 4.3 28.0 1.0
SD A:MET293 4.4 23.7 1.0
O A:SER489 4.4 25.3 1.0
CG A:PRO493 4.4 21.4 1.0
O A:PRO488 4.5 24.4 1.0
O A:HOH1002 4.9 41.1 1.0
NH1 A:ARG318 4.9 39.6 1.0
N A:ALA492 4.9 17.4 1.0
CG A:ARG318 4.9 23.3 1.0
CA A:ALA492 4.9 21.2 1.0
C A:SER489 5.0 23.9 1.0
NE2 A:GLN278 5.0 21.6 1.0

Magnesium binding site 4 out of 6 in 6ozw

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Magnesium binding site 4 out of 6 in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:23.0
occ:1.00
 O A:HOH827 2.8 17.5 1.0
O A:ILE193 2.9 14.4 1.0
OE1 A:GLU197 2.9 17.1 1.0
N A:GLU197 3.2 15.6 1.0
CB A:GLU197 3.5 14.7 1.0
CA A:GLU197 3.6 13.4 1.0
CG A:ARG196 3.6 14.9 1.0
CB A:ARG196 3.8 13.3 1.0
C A:ARG196 3.8 15.0 1.0
O A:PHE511 3.9 16.2 1.0
C A:ILE193 3.9 15.9 1.0
CD A:GLU197 4.0 15.9 1.0
CG A:ARG470 4.0 18.8 1.0
CG2 A:ILE193 4.0 14.2 1.0
CD A:ARG470 4.2 19.3 1.0
NE A:ARG470 4.2 21.0 1.0
CD A:PRO513 4.2 14.5 1.0
CA A:ARG196 4.3 13.7 1.0
CG A:GLU197 4.3 13.6 1.0
CA A:ILE193 4.3 12.8 1.0
CD1 A:ILE200 4.3 14.2 1.0
O A:ARG196 4.4 15.4 1.0
CB A:ARG470 4.5 16.4 1.0
CA A:ARG470 4.7 17.5 1.0
CB A:ILE193 4.8 11.0 1.0
N A:ARG196 4.9 15.2 1.0
C A:PHE511 4.9 15.9 1.0
CA A:GLU512 5.0 14.1 1.0
CD A:ARG196 5.0 15.9 1.0

Magnesium binding site 5 out of 6 in 6ozw

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Magnesium binding site 5 out of 6 in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:33.8
occ:1.00
 O A:HOH949 2.6 24.6 1.0
OD2 A:ASP161 2.9 31.1 1.0
NH1 A:ARG157 3.1 25.8 1.0
OD1 A:ASP161 3.2 25.4 1.0
CG A:ASP161 3.4 27.1 1.0
NH2 A:ARG184 3.5 31.3 1.0
CG A:ARG157 3.8 22.3 1.0
CD A:ARG157 3.9 25.6 1.0
CZ A:ARG157 4.2 28.9 1.0
NE A:ARG184 4.3 30.6 1.0
CZ A:ARG184 4.3 29.7 1.0
CG2 A:VAL185 4.3 21.4 1.0
CG2 A:THR490 4.4 22.4 1.0
NE A:ARG157 4.5 26.0 1.0
O A:HOH947 4.7 21.1 1.0
OE2 A:GLU541 4.7 27.3 1.0
CB A:ASP161 4.9 22.1 1.0
O A:HOH838 4.9 24.0 1.0
O A:HOH924 4.9 30.0 1.0
O A:HOH743 4.9 24.3 1.0

Magnesium binding site 6 out of 6 in 6ozw

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Magnesium binding site 6 out of 6 in the Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:47.3
occ:1.00
 O A:HOH814 2.7 35.8 1.0
ND2 A:ASN74 2.7 39.3 1.0
O A:HOH964 3.0 36.7 1.0
CB A:ASN74 3.4 29.3 1.0
CG A:ASN74 3.5 35.9 1.0
O A:HOH999 3.7 36.1 1.0
CA A:GLY79 3.7 27.4 1.0
CD1 A:ILE82 3.9 22.2 1.0
CG2 A:ILE82 4.4 23.8 1.0
CB A:ILE82 4.4 22.6 1.0
N A:GLY79 4.5 27.8 1.0
O A:GLY79 4.5 22.2 1.0
C A:GLY79 4.6 23.1 1.0
CG1 A:ILE82 4.7 23.1 1.0
OD1 A:ASN74 4.7 36.6 1.0
CA A:ASN74 4.9 26.3 1.0

Reference:

J.A.Jones, K.E.Hevener. Crystal Structure of the 65-Kilodalton Amino-Terminal Fragment of Dna Topoisomerase I From Streptococcus Mutans To Be Published.
Page generated: Tue Oct 1 13:43:54 2024

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