Magnesium in PDB 7r07: Abortive Infection Dna Polymerase Abik From Lactococcus Lactis

Protein crystallography data

The structure of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis, PDB code: 7r07 was solved by M.Figiel, M.Gapinska, M.Czarnocki-Cieciura, W.Zajko, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 3.10
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 200.99, 200.99, 570.72, 90, 90, 120
R / Rfree (%) 18.9 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis (pdb code 7r07). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis, PDB code: 7r07:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7r07

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Magnesium binding site 1 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:129.7
occ:1.00
 OD2 A:ASP247 2.3 118.3 1.0
O A:LEU164 2.4 114.7 1.0
OD2 A:ASP163 2.8 139.7 1.0
OD1 A:ASP163 2.9 136.9 1.0
CG A:ASP163 3.2 134.1 1.0
CG A:ASP247 3.5 113.0 1.0
C A:LEU164 3.6 95.7 1.0
N A:ASN166 4.0 103.2 1.0
O3' G:DC10 4.2 186.3 1.0
OD1 A:ASP247 4.2 120.7 1.0
N A:LEU164 4.4 90.2 1.0
CA A:SER165 4.4 91.9 1.0
N A:SER165 4.5 91.1 1.0
N A:PHE167 4.5 98.0 1.0
CA A:LEU164 4.6 84.0 1.0
C A:SER165 4.6 98.3 1.0
CB A:ASP247 4.6 96.4 1.0
CB A:ASP163 4.7 119.7 1.0
CA A:ASN166 4.8 108.5 1.0
NH2 A:ARG96 4.8 150.9 1.0
C A:ASP163 4.9 101.2 1.0

Magnesium binding site 2 out of 9 in 7r07

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Magnesium binding site 2 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:182.4
occ:1.00
 OD2 B:ASP247 2.5 113.5 1.0
OD1 B:ASP163 2.7 146.8 1.0
O B:LEU164 2.8 118.7 1.0
O3' H:DC10 2.9 177.9 1.0
OD2 B:ASP163 3.4 152.7 1.0
CG B:ASP163 3.4 143.6 1.0
CG B:ASP247 3.7 110.8 1.0
C B:LEU164 4.0 107.0 1.0
OD1 B:ASP247 4.2 115.5 1.0
C3' H:DC10 4.3 182.3 1.0
N B:ASN166 4.4 100.6 1.0
N B:LEU164 4.6 101.3 1.0
NH2 B:ARG96 4.7 147.4 1.0
CA B:SER165 4.8 100.8 1.0
N B:SER165 4.8 106.3 1.0
CA B:LEU164 4.9 96.0 1.0
CB B:ASP247 4.9 98.2 1.0
CB B:ASP163 4.9 122.6 1.0
C4' H:DC10 4.9 194.4 1.0
C B:SER165 5.0 102.0 1.0
C2' H:DC10 5.0 185.6 1.0

Magnesium binding site 3 out of 9 in 7r07

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Magnesium binding site 3 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:104.2
occ:1.00
 OD2 C:ASP247 2.4 99.4 1.0
O C:LEU164 2.5 102.0 1.0
OD1 C:ASP163 2.7 128.0 1.0
OD2 C:ASP163 3.0 127.1 1.0
CG C:ASP163 3.2 122.9 1.0
MG I:MG101 3.3 124.2 1.0
O3' I:DC10 3.4 219.8 1.0
CG C:ASP247 3.6 95.7 1.0
C C:LEU164 3.8 98.6 1.0
OD1 C:ASP247 4.2 102.2 1.0
N C:ASN166 4.3 110.7 1.0
CA C:SER165 4.5 104.9 1.0
N C:SER165 4.6 100.8 1.0
NH1 C:ARG96 4.6 143.9 1.0
N C:LEU164 4.7 87.7 1.0
CB C:ASP163 4.7 108.2 1.0
CA C:LEU164 4.8 90.8 1.0
C C:SER165 4.8 110.4 1.0
CB C:ASP247 4.8 82.7 1.0
C3' I:DC10 4.8 200.3 1.0
OD1 C:ASP248 4.9 122.7 1.0

Magnesium binding site 4 out of 9 in 7r07

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Magnesium binding site 4 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:103.9
occ:1.00
 O D:LEU164 2.0 163.9 1.0
OD2 D:ASP247 2.7 98.3 1.0
OD1 D:ASP163 2.8 144.3 1.0
MG D:MG602 3.2 136.9 1.0
C D:LEU164 3.2 117.3 1.0
CG D:ASP163 3.5 139.4 1.0
OD2 D:ASP163 3.5 143.8 1.0
N D:ASN166 3.7 96.5 1.0
CG D:ASP247 3.9 95.2 1.0
CA D:SER165 3.9 92.1 1.0
N D:SER165 4.0 96.8 1.0
C D:SER165 4.2 96.6 1.0
N D:LEU164 4.2 109.0 1.0
CA D:LEU164 4.3 105.7 1.0
OD1 D:ASP247 4.4 99.2 1.0
N D:PHE167 4.4 106.8 1.0
O3' J:DC10 4.7 197.2 1.0
CA D:ASN166 4.7 97.4 1.0
CB D:ASP163 4.7 126.2 1.0
CB D:PHE167 4.9 97.3 1.0
CB D:LEU164 4.9 95.0 1.0
C D:ASP163 5.0 107.5 1.0

Magnesium binding site 5 out of 9 in 7r07

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Magnesium binding site 5 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:136.9
occ:1.00
 O3' J:DC10 2.2 197.2 1.0
OD2 D:ASP163 2.8 143.8 1.0
OD1 D:ASP247 2.9 99.2 1.0
MG D:MG601 3.2 103.9 1.0
OD2 D:ASP248 3.2 134.3 1.0
OD1 D:ASP163 3.2 144.3 1.0
OD2 D:ASP247 3.2 98.3 1.0
CG D:ASP163 3.4 139.4 1.0
C3' J:DC10 3.4 192.9 1.0
CG D:ASP247 3.5 95.2 1.0
C4' J:DC10 3.9 192.8 1.0
C5' J:DC10 4.0 194.6 1.0
CG D:ASP248 4.1 127.8 1.0
NZ D:LYS281 4.4 124.0 1.0
OD1 D:ASP248 4.6 135.2 1.0
O D:LEU164 4.7 163.9 1.0
C2' J:DC10 4.7 191.7 1.0
CB D:ASP163 4.8 126.2 1.0
CB D:ASP247 5.0 86.6 1.0

Magnesium binding site 6 out of 9 in 7r07

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Magnesium binding site 6 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:128.6
occ:1.00
 OP1 K:DC11 2.3 302.3 1.0
O E:LEU164 2.5 98.2 1.0
OD2 E:ASP163 2.9 135.4 1.0
OD2 E:ASP247 3.1 98.8 1.0
OD1 E:ASP163 3.2 134.9 1.0
CG E:ASP163 3.4 130.2 1.0
P K:DC11 3.6 279.7 1.0
C E:LEU164 3.7 84.3 1.0
MG K:MG101 3.8 130.7 1.0
N E:ASN166 3.8 101.6 1.0
C5' K:DC11 3.9 252.8 1.0
O5' K:DC11 4.0 268.9 1.0
CA E:SER165 4.1 77.8 1.0
CG E:ASP247 4.3 98.4 1.0
C E:SER165 4.4 94.5 1.0
N E:SER165 4.4 76.3 1.0
OP2 K:DC11 4.6 277.3 1.0
O3' K:DC10 4.6 264.5 1.0
N E:LEU164 4.7 81.0 1.0
OD1 E:ASP247 4.7 109.0 1.0
CA E:ASN166 4.7 103.4 1.0
N E:PHE167 4.8 96.5 1.0
CA E:LEU164 4.8 77.1 1.0
CB E:ASP163 4.9 116.2 1.0
ND2 E:ASN278 5.0 109.9 1.0

Magnesium binding site 7 out of 9 in 7r07

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Magnesium binding site 7 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:125.7
occ:1.00
 O F:LEU164 2.0 164.5 1.0
OD2 F:ASP247 2.6 111.5 1.0
OD2 F:ASP163 2.9 139.0 1.0
OP1 L:DC10 3.0 207.6 1.0
C F:LEU164 3.2 126.2 1.0
C5' L:DC10 3.5 209.0 1.0
CG F:ASP163 3.5 134.3 1.0
OD1 F:ASP163 3.6 139.8 1.0
CG F:ASP247 3.7 103.2 1.0
O5' L:DC10 3.8 203.5 1.0
N F:ASN166 3.9 99.9 1.0
P L:DC10 4.0 199.0 1.0
N F:SER165 4.1 108.6 1.0
CA F:SER165 4.1 101.0 1.0
N F:LEU164 4.2 103.0 1.0
CA F:LEU164 4.2 110.2 1.0
OD1 F:ASP247 4.3 110.7 1.0
C F:SER165 4.4 103.3 1.0
N F:PHE167 4.5 103.1 1.0
CB F:LEU164 4.7 103.6 1.0
C4' L:DC10 4.7 207.1 1.0
CA F:ASN166 4.8 102.8 1.0
CB F:ASP163 4.8 119.7 1.0
OP2 L:DC10 4.9 194.1 1.0
O3' L:DC10 4.9 205.1 1.0
CB F:ASP247 4.9 86.0 1.0

Magnesium binding site 8 out of 9 in 7r07

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Magnesium binding site 8 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg101

b:124.2
occ:1.00
 O3' I:DC10 2.1 219.8 1.0
C4' I:DC10 2.5 197.3 1.0
C3' I:DC10 2.8 200.3 1.0
C5' I:DC10 2.8 189.9 1.0
OD1 C:ASP248 3.0 122.7 1.0
OD1 C:ASP163 3.2 128.0 1.0
MG C:MG601 3.3 104.2 1.0
NZ C:LYS281 3.7 134.2 1.0
OD1 C:ASP247 3.9 102.2 1.0
O4' I:DC10 3.9 192.7 1.0
OD2 C:ASP247 3.9 99.4 1.0
C2' I:DC10 4.0 197.6 1.0
O5' I:DC10 4.0 182.8 1.0
CG C:ASP248 4.1 113.3 1.0
CG C:ASP163 4.2 122.9 1.0
CG C:ASP247 4.3 95.7 1.0
OD2 C:ASP248 4.4 127.9 1.0
OD2 C:ASP163 4.6 127.1 1.0
C1' I:DC10 4.6 192.8 1.0
NH1 C:ARG96 4.7 143.9 1.0
OP1 I:DC10 4.9 171.9 1.0

Magnesium binding site 9 out of 9 in 7r07

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Magnesium binding site 9 out of 9 in the Abortive Infection Dna Polymerase Abik From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Abortive Infection Dna Polymerase Abik From Lactococcus Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg101

b:130.7
occ:1.00
 OP1 K:DC11 2.0 302.3 1.0
O3' K:DC10 2.1 264.5 1.0
P K:DC11 2.5 279.7 1.0
OD2 E:ASP248 2.6 131.0 1.0
OD1 E:ASP163 3.2 134.9 1.0
C3' K:DC10 3.2 224.3 1.0
OD1 E:ASP247 3.3 109.0 1.0
OP2 K:DC11 3.3 277.3 1.0
C4' K:DC10 3.5 202.1 1.0
C5' K:DC10 3.7 188.5 1.0
CG E:ASP248 3.7 126.5 1.0
MG E:MG601 3.8 128.6 1.0
OD2 E:ASP247 3.8 98.8 1.0
O5' K:DC11 3.9 268.9 1.0
CG E:ASP247 4.0 98.4 1.0
CG E:ASP163 4.0 130.2 1.0
NZ E:LYS281 4.1 121.1 1.0
C5' K:DC11 4.2 252.8 1.0
OD1 E:ASP248 4.3 137.3 1.0
OD2 E:ASP163 4.3 135.4 1.0
C2' K:DC10 4.5 211.2 1.0
O5' K:DC10 4.6 173.6 1.0
CE E:LYS281 4.7 122.8 1.0
CB E:ASP248 4.9 107.2 1.0
O4' K:DC10 5.0 192.1 1.0

Reference:

M.Figiel, M.Gapinska, M.Czarnocki-Cieciura, W.Zajko, M.Sroka, K.Skowronek, M.Nowotny. Mechanism of Protein-Primed Template-Independent Dna Synthesis By Abi Polymerases. Nucleic Acids Res. V. 50 10026 2022.
ISSN: ESSN 1362-4962
PubMed: 36107766
DOI: 10.1093/NAR/GKAC772
Page generated: Thu Apr 6 21:03:36 2023

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