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Magnesium in PDB 3akl: Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka

Enzymatic activity of Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka

All present enzymatic activity of Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka, PDB code: 3akl was solved by D.J.Kim, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.133, 74.835, 75.815, 78.84, 71.36, 85.44
R / Rfree (%) 18.9 / 28

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka (pdb code 3akl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka, PDB code: 3akl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3akl

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Magnesium binding site 1 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:61.2
occ:1.00
 OD2 A:ASP179 2.6 52.9 1.0
OD1 A:ASP179 2.6 49.5 1.0
CG A:ASP179 2.9 51.7 1.0
O2B A:ANP601 3.1 54.6 1.0
OG A:SER182 3.3 65.3 1.0
O1G A:ANP601 3.4 49.5 1.0
ND2 A:ASN21 3.7 64.0 1.0
O2G A:ANP601 3.9 56.0 1.0
CB A:SER182 3.9 57.8 1.0
OD1 A:ASP155 3.9 49.3 1.0
ND2 A:ASN160 4.0 44.6 1.0
PG A:ANP601 4.1 72.0 1.0
O3A A:ANP601 4.1 51.2 1.0
PB A:ANP601 4.2 49.6 1.0
N A:SER182 4.2 57.5 1.0
O A:ASP179 4.3 50.0 1.0
CB A:ASP179 4.4 49.6 1.0
CA A:SER182 4.6 50.8 1.0
OD1 A:ASN160 4.7 47.5 1.0
N3B A:ANP601 4.7 53.2 1.0
C A:GLY181 4.7 56.0 1.0
CG A:ASN160 4.7 46.6 1.0
C A:ASP179 4.9 50.4 1.0
CG A:ASP155 4.9 54.9 1.0
N A:GLY181 4.9 56.7 1.0
CG A:ASN21 5.0 63.4 1.0
CB A:ASP155 5.0 50.2 1.0
O A:ASP155 5.0 51.6 1.0

Magnesium binding site 2 out of 7 in 3akl

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Magnesium binding site 2 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:38.4
occ:1.00
 O1G A:ANP601 2.3 49.5 1.0
O3A A:ANP601 2.3 51.2 1.0
OD1 A:ASN160 2.7 47.5 1.0
O2A A:ANP601 3.0 46.3 1.0
PA A:ANP601 3.0 40.3 1.0
OD2 A:ASP179 3.1 52.9 1.0
PG A:ANP601 3.1 72.0 1.0
O3' A:ANP601 3.1 38.0 1.0
O5' A:ANP601 3.3 46.4 1.0
N3B A:ANP601 3.4 53.2 1.0
O3G A:ANP601 3.5 61.2 1.0
PB A:ANP601 3.5 49.6 1.0
C3' A:ANP601 3.6 45.9 1.0
CG A:ASP179 3.6 51.7 1.0
CB A:ASP179 3.8 49.6 1.0
CG A:ASN160 3.9 46.6 1.0
CE2 A:PHE178 4.1 43.5 1.0
O A:GLY159 4.2 51.6 1.0
C5' A:ANP601 4.3 44.5 1.0
C4' A:ANP601 4.3 45.2 1.0
O1A A:ANP601 4.4 51.0 1.0
O2B A:ANP601 4.4 54.6 1.0
O1B A:ANP601 4.4 42.5 1.0
OD1 A:ASP179 4.5 49.5 1.0
O2G A:ANP601 4.6 56.0 1.0
NE2 A:HIS157 4.7 43.3 1.0
ND2 A:ASN160 4.7 44.6 1.0
CD2 A:PHE178 4.7 46.5 1.0
CA A:GLY19 4.8 46.6 1.0
CA A:ASN160 4.8 45.8 1.0
C2' A:ANP601 4.9 45.1 1.0
CB A:ASN160 4.9 52.3 1.0
C A:GLY159 5.0 47.8 1.0
CE1 A:HIS157 5.0 41.1 1.0

Magnesium binding site 3 out of 7 in 3akl

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Magnesium binding site 3 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:60.5
occ:1.00
 OD1 B:ASP179 2.6 45.4 1.0
O1G B:ANP600 2.6 59.5 1.0
OG B:SER182 2.9 63.5 1.0
O2B B:ANP600 2.9 54.5 1.0
OD2 B:ASP179 3.1 48.3 1.0
CG B:ASP179 3.2 48.7 1.0
ND2 B:ASN21 3.3 56.8 1.0
PG B:ANP600 3.7 67.1 1.0
O3G B:ANP600 4.0 51.1 1.0
PB B:ANP600 4.1 53.8 1.0
CB B:SER182 4.1 58.2 1.0
N3B B:ANP600 4.2 45.8 1.0
N B:SER182 4.2 51.5 1.0
ND2 B:ASN160 4.2 50.6 1.0
OD1 B:ASP155 4.3 55.2 1.0
O B:ASP179 4.6 46.6 1.0
C B:GLY181 4.6 53.7 1.0
CG B:ASN21 4.6 66.2 1.0
CB B:ASP179 4.7 43.1 1.0
CA B:GLY181 4.7 49.1 1.0
CA B:SER182 4.7 55.6 1.0
N B:GLY181 4.8 48.6 1.0
O1B B:ANP600 4.8 48.6 1.0
NZ B:LYS37 4.9 44.2 1.0

Magnesium binding site 4 out of 7 in 3akl

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Magnesium binding site 4 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:48.8
occ:1.00
 O2A B:ANP600 2.3 45.4 1.0
N3B B:ANP600 2.5 45.8 1.0
OD1 B:ASN160 2.5 46.1 1.0
O3G B:ANP600 2.7 51.1 1.0
O3' B:ANP600 2.9 37.0 1.0
OD2 B:ASP179 2.9 48.3 1.0
PG B:ANP600 3.2 67.1 1.0
O B:GLY159 3.3 41.3 1.0
C3' B:ANP600 3.5 44.0 1.0
PA B:ANP600 3.7 42.3 1.0
CG B:ASN160 3.7 47.2 1.0
O2G B:ANP600 3.9 53.7 1.0
PB B:ANP600 3.9 53.8 1.0
CG B:ASP179 4.0 48.7 1.0
O3A B:ANP600 4.0 46.7 1.0
CE2 B:PHE178 4.2 47.7 1.0
C B:GLY159 4.3 45.6 1.0
CB B:ASP179 4.3 43.1 1.0
C5' B:ANP600 4.3 34.9 1.0
O5' B:ANP600 4.3 35.1 1.0
C4' B:ANP600 4.4 38.8 1.0
ND2 B:ASN160 4.5 50.6 1.0
O1G B:ANP600 4.5 59.5 1.0
CE1 B:HIS157 4.5 48.8 1.0
O2B B:ANP600 4.5 54.5 1.0
NE2 B:HIS157 4.6 47.7 1.0
CA B:ASN160 4.7 42.2 1.0
O1A B:ANP600 4.8 43.0 1.0
CA B:GLY19 4.8 44.0 1.0
CB B:ASN160 4.8 46.1 1.0
C2' B:ANP600 4.8 40.9 1.0
N B:ASN160 4.9 46.7 1.0
O1B B:ANP600 4.9 48.6 1.0
CD2 B:PHE178 5.0 47.2 1.0

Magnesium binding site 5 out of 7 in 3akl

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Magnesium binding site 5 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg400

b:57.8
occ:1.00
 OD2 C:ASP179 2.3 70.8 1.0
O3B C:ADP500 2.4 64.1 1.0
O2A C:ADP500 2.4 78.2 1.0
OD1 C:ASN160 2.5 53.9 1.0
CG C:ASP179 3.5 70.1 1.0
CG C:ASN160 3.7 57.4 1.0
NE2 C:HIS157 3.7 58.4 1.0
PB C:ADP500 3.8 71.6 1.0
CE1 C:HIS157 3.9 57.1 1.0
PA C:ADP500 3.9 75.5 1.0
O C:GLY159 4.1 60.9 1.0
ND2 C:ASN160 4.1 66.1 1.0
O3A C:ADP500 4.3 62.9 1.0
CB C:ASP179 4.4 65.2 1.0
OD1 C:ASP179 4.4 74.3 1.0
C5' C:ADP500 4.4 63.0 1.0
O1B C:ADP500 4.5 66.4 1.0
O5' C:ADP500 4.6 62.9 1.0
CA C:GLY19 4.7 62.2 1.0
C C:GLY159 4.8 59.1 1.0
O2B C:ADP500 4.9 67.2 1.0
CB C:ASN160 4.9 55.3 1.0
O1A C:ADP500 5.0 63.8 1.0

Magnesium binding site 6 out of 7 in 3akl

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Magnesium binding site 6 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:68.2
occ:1.00
 ND2 D:ASN21 3.0 69.8 1.0
OD1 D:ASP179 3.0 43.1 1.0
N3B D:ANP602 3.3 60.0 1.0
O2B D:ANP602 3.8 59.7 1.0
OG D:SER182 3.8 67.2 1.0
CG D:ASN21 4.0 71.7 1.0
CA D:GLY181 4.0 50.7 1.0
N D:SER182 4.0 58.9 1.0
CB D:ASN21 4.0 70.1 1.0
C D:GLY181 4.1 54.6 1.0
CG D:ASP179 4.1 48.2 1.0
PB D:ANP602 4.2 54.2 1.0
O3G D:ANP602 4.3 64.8 1.0
NZ D:LYS37 4.5 45.7 1.0
PG D:ANP602 4.5 65.7 1.0
N D:GLY181 4.5 49.8 1.0
OD2 D:ASP179 4.6 46.2 1.0
CB D:SER182 4.8 54.8 1.0
CA D:SER182 4.9 56.2 1.0
O D:GLY181 4.9 49.0 1.0

Magnesium binding site 7 out of 7 in 3akl

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Magnesium binding site 7 out of 7 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg406

b:51.9
occ:1.00
 O2G D:ANP602 2.3 53.4 1.0
OD2 D:ASP179 3.0 46.2 1.0
O3A D:ANP602 3.1 49.5 1.0
OD1 D:ASN160 3.2 48.0 1.0
O3' D:ANP602 3.4 45.0 1.0
O D:GLY159 3.5 47.7 1.0
PG D:ANP602 3.5 65.7 1.0
C3' D:ANP602 3.6 49.9 1.0
O1G D:ANP602 3.8 68.3 1.0
O5' D:ANP602 3.9 48.2 1.0
PA D:ANP602 4.1 45.4 1.0
CG D:ASP179 4.1 48.2 1.0
C D:GLY159 4.2 50.2 1.0
PB D:ANP602 4.2 54.2 1.0
N3B D:ANP602 4.2 60.0 1.0
NE2 D:HIS157 4.3 47.3 1.0
CG D:ASN160 4.4 52.8 1.0
C5' D:ANP602 4.4 42.1 1.0
CE2 D:PHE178 4.4 42.7 1.0
O1B D:ANP602 4.5 52.1 1.0
CE1 D:HIS157 4.5 46.1 1.0
C4' D:ANP602 4.6 52.0 1.0
CB D:ASP179 4.6 44.8 1.0
O2A D:ANP602 4.6 42.3 1.0
CA D:ASN160 4.7 45.8 1.0
N D:ASN160 4.7 49.1 1.0
C2' D:ANP602 4.8 51.3 1.0
O3G D:ANP602 4.8 64.8 1.0
CD2 D:PHE178 5.0 39.5 1.0
CA D:GLY159 5.0 45.7 1.0

Reference:

D.J.Kim, K.-S.Park, J.-H.Kim, S.-H.Yang, J.Y.Yoon, B.-G.Han, H.S.Kim, S.J.Lee, J.Y.Jang, K.H.Kim, M.J.Kim, J.-S.Song, H.-J.Kim, C.-M.Park, S.-K.Lee, B.I.Lee, S.W.Suh. Helicobacter Pylori Proinflammatory Protein Up-Regulates Nf-Kappab As A Cell-Translocating Ser/Thr Kinase Proc.Natl.Acad.Sci.Usa V. 107 21418 2010.
ISSN: ISSN 0027-8424
PubMed: 21098302
DOI: 10.1073/PNAS.1010153107
Page generated: Sun Aug 10 17:30:01 2025

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