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Magnesium in PDB 4r39: Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase

Enzymatic activity of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase

All present enzymatic activity of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase:
2.7.13.3;

Protein crystallography data

The structure of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase, PDB code: 4r39 was solved by D.R.Tomchick, G.Rivera-Cancel, K.H.Gardner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.25 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.503, 120.503, 192.304, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase (pdb code 4r39). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase, PDB code: 4r39:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4r39

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Magnesium binding site 1 out of 4 in the Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:3.3
occ:1.00
 O2G A:ANP402 2.0 5.3 1.0
OD1 A:ASN250 2.0 17.2 1.0
O A:HOH502 2.1 9.0 1.0
O A:HOH501 2.1 18.3 1.0
O1A A:ANP402 2.1 16.5 1.0
O2B A:ANP402 2.2 6.3 1.0
HD21 A:ASN250 2.9 20.3 1.0
CG A:ASN250 3.0 16.7 1.0
ND2 A:ASN250 3.3 16.9 1.0
PB A:ANP402 3.3 9.8 1.0
PA A:ANP402 3.3 16.0 1.0
PG A:ANP402 3.3 19.6 1.0
HA3 A:GLY300 3.5 27.9 1.0
O3A A:ANP402 3.6 15.1 1.0
HE2 A:HIS254 3.6 25.0 1.0
O3G A:ANP402 3.9 10.9 1.0
N3B A:ANP402 3.9 12.4 1.0
O5' A:ANP402 4.0 16.9 1.0
OE1 A:GLU246 4.0 24.1 1.0
HD22 A:ASN250 4.1 20.3 1.0
O A:GLU246 4.1 16.9 1.0
HA A:ASN250 4.2 18.9 1.0
HH22 A:ARG174 4.3 46.6 1.0
HNB1 A:ANP402 4.3 14.9 1.0
CB A:ASN250 4.3 15.9 1.0
NE2 A:HIS254 4.4 20.9 1.0
CA A:GLY300 4.4 23.2 1.0
O1G A:ANP402 4.5 14.9 1.0
HG A:SER171 4.5 27.4 1.0
HD2 A:HIS254 4.5 24.6 1.0
O2A A:ANP402 4.5 10.1 1.0
O1B A:ANP402 4.5 20.0 1.0
H A:GLY300 4.6 28.8 1.0
HB A:THR249 4.7 30.1 1.0
OE1 A:GLN253 4.7 31.9 1.0
HA A:GLU246 4.7 18.8 1.0
CA A:ASN250 4.7 15.7 1.0
H A:ASN250 4.8 18.3 1.0
HB2 A:ASN250 4.8 19.1 1.0
HA2 A:GLY300 4.8 27.9 1.0
H3' A:ANP402 4.8 11.8 1.0
CD2 A:HIS254 4.8 20.5 1.0
HE1 A:TRP293 4.9 35.2 1.0
HH21 A:ARG175 4.9 24.8 1.0
HB3 A:GLU246 4.9 19.4 1.0
O A:HOH506 4.9 17.5 1.0
N A:ASN250 4.9 15.2 1.0
HB3 A:ASN250 4.9 19.1 1.0
NH2 A:ARG174 4.9 38.9 1.0

Magnesium binding site 2 out of 4 in 4r39

Go back to Magnesium Binding Sites List in 4r39
Magnesium binding site 2 out of 4 in the Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:20.2
occ:1.00
 O1A B:ANP402 1.9 19.2 1.0
O2G B:ANP402 1.9 36.8 1.0
O B:HOH502 2.1 14.6 1.0
O B:HOH501 2.1 20.1 1.0
OD1 B:ASN250 2.1 23.5 1.0
O2B B:ANP402 2.1 24.3 1.0
HD21 B:ASN250 3.0 31.4 1.0
CG B:ASN250 3.1 22.2 1.0
PA B:ANP402 3.1 19.6 1.0
PB B:ANP402 3.2 23.4 1.0
PG B:ANP402 3.3 34.0 1.0
HA3 B:GLY300 3.4 41.8 1.0
ND2 B:ASN250 3.4 26.1 1.0
O3A B:ANP402 3.6 13.6 1.0
HE2 B:HIS254 3.8 33.3 1.0
O B:HOH528 3.8 21.5 1.0
N3B B:ANP402 3.8 33.5 1.0
O3G B:ANP402 3.9 5.7 1.0
O5' B:ANP402 4.0 29.1 1.0
OE1 B:GLU246 4.1 30.8 1.0
O B:GLU246 4.2 19.0 1.0
HD22 B:ASN250 4.2 31.4 1.0
O2A B:ANP402 4.3 18.6 1.0
HA B:ASN250 4.3 23.0 1.0
HG B:SER171 4.3 41.0 1.0
CA B:GLY300 4.3 34.8 1.0
O1G B:ANP402 4.4 30.1 1.0
HNB1 B:ANP402 4.4 40.1 1.0
CB B:ASN250 4.4 20.2 1.0
OE1 B:GLN253 4.5 34.6 1.0
O1B B:ANP402 4.5 22.6 1.0
NE2 B:HIS254 4.5 27.8 1.0
HH21 B:ARG175 4.6 40.5 1.0
H B:GLY300 4.7 42.4 1.0
HB3 B:GLU246 4.7 26.8 1.0
HD2 B:HIS254 4.7 30.7 1.0
HA B:GLU246 4.7 23.4 1.0
HA2 B:GLY300 4.7 41.8 1.0
CA B:ASN250 4.7 19.2 1.0
H3' B:ANP402 4.8 27.2 1.0
H B:ASN250 4.8 23.4 1.0
OG1 B:THR249 4.8 29.6 1.0
HE1 B:TRP293 4.9 36.4 1.0
HG1 B:THR249 4.9 35.6 1.0
HB2 B:ASN250 4.9 24.3 1.0
OG B:SER171 5.0 34.2 1.0
N B:ASN250 5.0 19.5 1.0
HB3 B:ASN250 5.0 24.3 1.0

Magnesium binding site 3 out of 4 in 4r39

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Magnesium binding site 3 out of 4 in the Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:28.6
occ:1.00
 O2B C:ANP402 2.0 32.6 1.0
O C:HOH501 2.1 32.8 1.0
OD1 C:ASN250 2.1 30.9 1.0
O C:HOH502 2.1 41.0 1.0
O2G C:ANP402 2.1 45.6 1.0
O1A C:ANP402 2.3 44.5 1.0
HD21 C:ASN250 2.9 37.7 1.0
CG C:ASN250 3.0 31.9 1.0
PB C:ANP402 3.2 35.4 1.0
ND2 C:ASN250 3.3 31.4 1.0
HA3 C:GLY300 3.3 59.5 1.0
PA C:ANP402 3.4 36.2 1.0
PG C:ANP402 3.4 31.9 1.0
O3A C:ANP402 3.4 55.3 1.0
HE2 C:HIS254 3.8 41.7 1.0
N3B C:ANP402 3.9 19.8 1.0
O3G C:ANP402 3.9 46.3 1.0
O5' C:ANP402 4.1 26.6 1.0
HD22 C:ASN250 4.1 37.7 1.0
O C:GLU246 4.1 35.5 1.0
OE1 C:GLU246 4.2 40.2 1.0
HA C:ASN250 4.2 32.1 1.0
CA C:GLY300 4.2 49.6 1.0
HNB1 C:ANP402 4.3 23.7 1.0
O C:HOH540 4.3 36.0 1.0
HG C:SER171 4.3 55.5 1.0
OE1 C:GLN253 4.3 45.2 1.0
CB C:ASN250 4.3 29.9 1.0
O1B C:ANP402 4.4 17.7 1.0
HA2 C:GLY300 4.5 59.5 1.0
HD2 C:HIS254 4.5 40.6 1.0
NE2 C:HIS254 4.5 34.8 1.0
O1G C:ANP402 4.6 44.7 1.0
HH21 C:ARG175 4.6 54.2 1.0
H C:ASN250 4.6 31.7 1.0
CA C:ASN250 4.6 26.7 1.0
H C:GLY300 4.6 59.5 1.0
O2A C:ANP402 4.6 39.0 1.0
HA C:GLU246 4.7 39.7 1.0
HB3 C:GLU246 4.7 40.8 1.0
N C:ASN250 4.8 26.4 1.0
HB C:THR249 4.8 46.5 1.0
HB2 C:ASN250 4.8 35.9 1.0
OG C:SER171 4.9 46.2 1.0
HB3 C:ASN250 4.9 35.9 1.0
CD2 C:HIS254 4.9 33.9 1.0
H3' C:ANP402 4.9 42.7 1.0
N C:GLY300 5.0 49.6 1.0
C C:GLU246 5.0 33.7 1.0

Magnesium binding site 4 out of 4 in 4r39

Go back to Magnesium Binding Sites List in 4r39
Magnesium binding site 4 out of 4 in the Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Histidine Kinase Domain From Erythrobacter Litoralis EL346 Blue-Light Activated Histidine Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:16.4
occ:1.00
 O2G D:ANP402 2.0 21.9 1.0
O D:HOH501 2.1 21.4 1.0
OD1 D:ASN250 2.1 22.1 1.0
O D:HOH502 2.1 7.6 1.0
O1A D:ANP402 2.2 18.4 1.0
O2B D:ANP402 2.3 7.0 1.0
HD21 D:ASN250 2.9 22.5 1.0
CG D:ASN250 2.9 18.7 1.0
ND2 D:ASN250 3.3 18.8 1.0
HA3 D:GLY300 3.3 21.3 1.0
PG D:ANP402 3.4 13.5 1.0
PA D:ANP402 3.5 14.0 1.0
PB D:ANP402 3.5 17.9 1.0
OE1 D:GLU246 3.8 29.2 1.0
O3G D:ANP402 3.8 25.3 1.0
HE2 D:HIS254 3.9 25.3 1.0
O3A D:ANP402 3.9 22.3 1.0
O D:GLU246 3.9 21.1 1.0
HD22 D:ASN250 4.1 22.5 1.0
N3B D:ANP402 4.1 9.0 1.0
HA D:ASN250 4.1 25.0 1.0
OE1 D:GLN253 4.2 29.6 1.0
HG D:SER171 4.2 38.5 1.0
O D:HOH529 4.2 22.4 1.0
CA D:GLY300 4.3 17.7 1.0
CB D:ASN250 4.3 17.8 1.0
O5' D:ANP402 4.3 14.3 1.0
HH21 D:ARG175 4.4 24.1 1.0
O1G D:ANP402 4.4 10.4 1.0
HA2 D:GLY300 4.6 21.3 1.0
H D:GLY300 4.6 23.0 1.0
HA D:GLU246 4.6 22.4 1.0
CA D:ASN250 4.6 20.8 1.0
O2A D:ANP402 4.6 24.6 1.0
H D:ASN250 4.6 23.0 1.0
HB3 D:GLU246 4.6 24.5 1.0
NE2 D:HIS254 4.6 21.1 1.0
HB2 D:ASN250 4.7 21.4 1.0
HNB1 D:ANP402 4.7 10.8 1.0
HD2 D:HIS254 4.7 25.0 1.0
HH22 D:ARG175 4.7 24.1 1.0
O1B D:ANP402 4.7 14.8 1.0
N D:ASN250 4.8 19.2 1.0
OG D:SER171 4.8 32.1 1.0
HG22 D:THR249 4.9 22.3 1.0
C D:GLU246 4.9 19.9 1.0
NH2 D:ARG175 4.9 20.1 1.0
HB3 D:ASN250 4.9 21.4 1.0
HB D:THR249 4.9 21.6 1.0
N D:GLY300 4.9 19.2 1.0
CD D:GLU246 5.0 27.2 1.0
HE1 D:TRP293 5.0 20.8 1.0

Reference:

G.Rivera-Cancel, W.H.Ko, D.R.Tomchick, F.Correa, K.H.Gardner. Full-Length Structure of A Monomeric Histidine Kinase Reveals Basis For Sensory Regulation Proc.Natl.Acad.Sci.Usa 2014.
ISSN: ESSN 1091-6490
Page generated: Tue Aug 20 02:48:15 2024

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