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Magnesium in PDB 4j6w: Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp

Protein crystallography data

The structure of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp, PDB code: 4j6w was solved by A.D.Nikulin, V.Murina, N.Lekontseva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.280, 74.550, 109.610, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 4j6w:

The structure of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp (pdb code 4j6w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp, PDB code: 4j6w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4j6w

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Magnesium binding site 1 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:40.1
occ:1.00
 NZ A:LYS56 2.5 14.3 1.0
O A:ASP40 2.8 19.8 1.0
OD2 A:ASP9 3.0 33.9 1.0
CD1 A:PHE39 3.2 18.7 1.0
O A:HOH250 3.2 38.8 1.0
CE1 A:PHE39 3.5 21.2 1.0
C A:ASP40 3.6 20.4 1.0
CE A:LYS56 3.6 16.2 1.0
CG A:ASP9 4.0 34.1 1.0
OE1 A:GLN8 4.1 20.2 1.0
CD1 A:LEU12 4.2 10.0 1.0
N A:GLN41 4.2 21.0 1.0
CA A:GLN41 4.2 22.7 1.0
CD A:GLN8 4.4 20.7 1.0
CG A:PHE39 4.4 19.2 1.0
CA A:ASP40 4.4 20.2 1.0
O A:GLN41 4.7 17.8 1.0
C A:GLN41 4.7 25.9 1.0
N A:ASP40 4.7 18.4 1.0
OD1 A:ASP9 4.7 37.6 1.0
CE1 A:HIS5 4.7 37.9 0.6
CG A:GLN8 4.7 17.9 1.0
CZ A:PHE39 4.9 16.9 1.0
CD A:LYS56 4.9 13.3 1.0
CB A:PHE39 4.9 17.6 1.0
CA A:ASP9 4.9 21.3 1.0
CB A:ASP9 4.9 21.8 1.0
NE2 A:GLN8 5.0 22.0 1.0

Magnesium binding site 2 out of 8 in 4j6w

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Magnesium binding site 2 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:40.6
occ:1.00
 OP1 D:C101 2.0 40.2 0.6
O B:HOH222 2.0 39.7 1.0
O2A B:CTP101 2.4 33.3 0.8
O D:HOH226 2.5 36.7 1.0
P D:C101 2.9 46.7 0.6
O3A B:CTP101 2.9 35.6 0.8
O B:HOH236 2.9 40.6 1.0
O2B B:CTP101 3.2 38.8 0.8
PA B:CTP101 3.2 28.1 0.8
O5' D:C101 3.2 37.2 0.6
OP2 D:C101 3.4 41.5 0.6
C3' D:C101 3.6 27.9 0.6
C5' D:C101 3.6 32.3 0.6
PB B:CTP101 3.7 43.2 0.8
O1G B:CTP101 4.0 34.4 0.8
O3' D:C101 4.0 28.1 0.6
OP3 D:C101 4.2 34.8 0.6
O1A B:CTP101 4.2 15.6 0.8
C4' D:C101 4.2 26.2 0.6
O5' B:CTP101 4.4 20.8 0.8
O B:HOH237 4.5 48.4 1.0
O3B B:CTP101 4.6 36.8 0.8
C6 D:C101 4.6 30.2 0.6
C5' B:CTP101 4.6 22.1 0.8
CE1 B:PHE42 4.6 29.9 1.0
OP2 A:C102 4.7 37.2 0.7
C2' D:C101 4.7 27.8 0.6
MG D:MG105 4.8 43.3 1.0
O1B B:CTP101 4.9 28.4 0.8
OP3 A:C102 4.9 38.5 0.7
PG B:CTP101 4.9 39.4 0.8
C5 D:C101 4.9 30.1 0.6

Magnesium binding site 3 out of 8 in 4j6w

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Magnesium binding site 3 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:42.6
occ:1.00
 OP2 C:C102 2.4 46.1 0.7
C5' E:C101 2.8 24.9 0.8
OP2 E:C101 3.1 34.9 0.8
O3' E:C101 3.1 19.5 0.8
O A:HOH260 3.1 38.6 1.0
O B:HOH238 3.1 38.0 1.0
O2B F:CDP101 3.3 43.8 0.8
C4' E:C101 3.4 25.3 0.8
O3G B:CTP101 3.4 41.0 0.8
MG C:MG104 3.6 49.7 1.0
C3' E:C101 3.6 26.1 0.8
P C:C102 3.7 51.5 0.7
O5' E:C101 3.7 23.4 0.8
ND1 C:HIS57 4.0 14.9 1.0
CB E:HIS57 4.0 11.1 1.0
O E:HOH214 4.0 20.8 1.0
P E:C101 4.1 36.3 0.8
MG E:MG104 4.1 38.2 1.0
MG E:MG105 4.1 40.3 1.0
CB C:HIS57 4.2 12.2 1.0
PB F:CDP101 4.2 36.0 0.8
OP3 C:C102 4.3 37.5 0.7
CG C:HIS57 4.3 12.6 1.0
O E:HOH229 4.3 33.6 1.0
O5' C:C102 4.4 33.4 0.7
PG B:CTP101 4.4 39.4 0.8
O2G B:CTP101 4.5 41.9 0.8
O3B F:CDP101 4.5 32.9 0.8
CA E:HIS57 4.5 11.9 1.0
O1B F:CDP101 4.6 37.2 0.8
O4' E:C101 4.8 21.8 0.8
CE1 C:HIS57 4.8 12.6 1.0
O1G B:CTP101 4.9 34.4 0.8
OP1 C:C102 5.0 47.9 0.7

Magnesium binding site 4 out of 8 in 4j6w

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Magnesium binding site 4 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:49.7
occ:1.00
 O1G B:CTP101 2.0 34.4 0.8
O2B F:CDP101 2.2 43.8 0.8
O B:HOH237 2.4 48.4 1.0
PG B:CTP101 2.6 39.4 0.8
O A:HOH260 2.6 38.6 1.0
O2G B:CTP101 2.8 41.9 0.8
O3G B:CTP101 2.9 41.0 0.8
OP2 C:C102 2.9 46.1 0.7
P C:C102 3.3 51.5 0.7
OP2 D:C101 3.3 41.5 0.6
NA F:NA105 3.4 55.6 1.0
OP1 C:C102 3.4 47.9 0.7
MG C:MG103 3.6 42.6 1.0
O B:HOH236 3.6 40.6 1.0
PB F:CDP101 3.6 36.0 0.8
O3A F:CDP101 4.0 31.0 0.8
O3B B:CTP101 4.2 36.8 0.8
MG E:MG104 4.2 38.2 1.0
OP2 A:C102 4.3 37.2 0.7
OP3 C:C102 4.3 37.5 0.7
O1B F:CDP101 4.4 37.2 0.8
OP1 A:C102 4.5 41.9 0.7
O B:HOH238 4.5 38.0 1.0
MG D:MG105 4.6 43.3 1.0
O5' C:C102 4.6 33.4 0.7
O3B F:CDP101 4.7 32.9 0.8
OP2 E:C101 4.7 34.9 0.8
O2B B:CTP101 4.7 38.8 0.8
P D:C101 4.7 46.7 0.6
O C:HOH224 4.8 44.9 1.0
P A:C102 4.8 39.8 0.7
O E:HOH229 5.0 33.6 1.0
O1A F:CDP101 5.0 28.9 0.8

Magnesium binding site 5 out of 8 in 4j6w

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Magnesium binding site 5 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg104

b:21.9
occ:1.00
 O D:PHE42 2.9 12.1 1.0
N D:HIS57 3.1 11.2 1.0
O3' F:CDP101 3.1 17.1 0.8
ND1 D:HIS57 3.1 10.5 1.0
O2' F:CDP101 3.2 16.4 0.8
N D:LYS56 3.2 9.5 1.0
O4' D:C101 3.2 33.1 0.6
C4' D:C101 3.3 26.2 0.6
CG D:HIS57 3.6 11.3 1.0
CB D:LYS56 3.7 15.6 1.0
CB D:HIS57 3.7 11.8 1.0
CA D:LYS56 3.7 11.6 1.0
C D:PHE42 3.8 19.1 1.0
C D:LYS56 3.8 12.5 1.0
C D:TYR55 3.9 10.6 1.0
C2' F:CDP101 3.9 22.9 0.8
CD2 D:TYR55 4.0 8.7 1.0
CA D:HIS57 4.0 10.3 1.0
CE1 D:HIS57 4.0 10.5 1.0
CB D:TYR55 4.0 9.3 1.0
CA D:PHE42 4.0 21.9 1.0
CB D:PHE42 4.0 22.6 1.0
CA D:TYR55 4.1 11.4 1.0
C3' F:CDP101 4.1 21.4 0.8
C5' D:C101 4.1 32.3 0.6
C1' D:C101 4.2 25.4 0.6
O2' D:C101 4.3 26.4 0.6
CD1 D:PHE42 4.4 24.9 1.0
C3' D:C101 4.4 27.9 0.6
CG D:TYR55 4.5 10.6 1.0
C2' D:C101 4.6 27.8 0.6
O3' D:C101 4.6 28.1 0.6
CD2 D:HIS57 4.6 11.0 1.0
CG D:PHE42 4.7 25.2 1.0
O D:TYR55 4.7 7.5 1.0
NE2 D:HIS57 4.8 12.5 1.0
CG D:LYS56 4.8 12.9 1.0
O5' D:C101 4.9 37.2 0.6

Magnesium binding site 6 out of 8 in 4j6w

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Magnesium binding site 6 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg105

b:43.3
occ:1.00
 O B:HOH220 2.2 28.7 1.0
O2B B:CTP101 2.3 38.8 0.8
OP2 D:C101 2.4 41.5 0.6
O5' D:C101 2.5 37.2 0.6
O2G B:CTP101 2.9 41.9 0.8
O3' F:CDP101 2.9 17.1 0.8
P D:C101 3.0 46.7 0.6
C5' F:CDP101 3.2 24.8 0.8
C3' F:CDP101 3.5 21.4 0.8
O3A F:CDP101 3.6 31.0 0.8
C4' F:CDP101 3.6 26.5 0.8
PB B:CTP101 3.6 43.2 0.8
OP3 D:C101 3.7 34.8 0.6
C5' D:C101 3.8 32.3 0.6
PG B:CTP101 3.8 39.4 0.8
O1G B:CTP101 4.0 34.4 0.8
O3' D:C101 4.0 28.1 0.6
O3B B:CTP101 4.1 36.8 0.8
O1B B:CTP101 4.1 28.4 0.8
CB D:HIS57 4.2 11.8 1.0
O1B F:CDP101 4.2 37.2 0.8
O5' F:CDP101 4.2 29.2 0.8
NA F:NA105 4.3 55.6 1.0
C4' D:C101 4.3 26.2 0.6
OP1 D:C101 4.3 40.2 0.6
ND1 D:HIS57 4.3 10.5 1.0
O2B F:CDP101 4.4 43.8 0.8
PB F:CDP101 4.4 36.0 0.8
O F:HOH203 4.5 23.4 1.0
C3' D:C101 4.6 27.9 0.6
CG D:HIS57 4.6 11.3 1.0
O F:HOH228 4.6 39.7 1.0
MG C:MG104 4.6 49.7 1.0
PA F:CDP101 4.7 28.6 0.8
MG B:MG102 4.8 40.6 1.0
O3A B:CTP101 4.9 35.6 0.8
C2' F:CDP101 4.9 22.9 0.8

Magnesium binding site 7 out of 8 in 4j6w

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Magnesium binding site 7 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg104

b:38.2
occ:1.00
 O A:HOH260 2.0 38.6 1.0
OP1 E:C101 2.2 27.4 0.8
P E:C101 2.7 36.3 0.8
C5' E:C101 2.8 24.9 0.8
O A:HOH233 2.8 31.4 1.0
OP2 E:C101 2.9 34.9 0.8
OP1 A:C102 2.9 41.9 0.7
O5' E:C101 2.9 23.4 0.8
OP2 C:C102 3.8 46.1 0.7
CE1 E:PHE42 3.9 31.5 1.0
MG C:MG103 4.1 42.6 1.0
OP3 E:C101 4.1 20.6 0.8
O E:HOH229 4.1 33.6 1.0
MG C:MG104 4.2 49.7 1.0
C4' E:C101 4.2 25.3 0.8
P A:C102 4.3 39.8 0.7
CD1 E:PHE42 4.4 28.2 1.0
OP3 C:C102 4.4 37.5 0.7
O B:HOH237 4.6 48.4 1.0
C6 E:C101 4.7 29.2 0.8
O3G B:CTP101 4.7 41.0 0.8
O4' E:C101 4.7 21.8 0.8
C3' E:C101 4.8 26.1 0.8
C3' A:C102 4.8 31.5 0.7
P C:C102 4.8 51.5 0.7
OP3 A:C102 4.8 38.5 0.7
O3' A:C102 4.9 29.8 0.7
CZ E:PHE42 5.0 31.1 1.0

Magnesium binding site 8 out of 8 in 4j6w

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Magnesium binding site 8 out of 8 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg105

b:40.3
occ:1.00
 O E:HOH229 1.9 33.6 1.0
O A:HOH249 2.5 25.4 1.0
OP2 E:C101 2.8 34.9 0.8
O3G B:CTP101 3.0 41.0 0.8
O3' A:C102 3.2 29.8 0.7
CB E:HIS57 3.4 11.1 1.0
CG E:HIS57 3.5 12.0 1.0
ND1 E:HIS57 3.7 11.6 1.0
O B:HOH238 3.7 38.0 1.0
CB A:HIS57 3.8 12.1 1.0
P E:C101 4.1 36.3 0.8
OP3 E:C101 4.1 20.6 0.8
MG C:MG103 4.1 42.6 1.0
O A:HOH240 4.2 35.3 1.0
CD2 E:HIS57 4.2 10.1 1.0
CA A:HIS57 4.2 8.8 1.0
O A:HOH260 4.2 38.6 1.0
O A:HIS57 4.3 8.6 1.0
OP2 A:C102 4.3 37.2 0.7
PG B:CTP101 4.4 39.4 0.8
OP1 A:C102 4.4 41.9 0.7
CE1 E:HIS57 4.4 7.9 1.0
O B:HOH209 4.5 31.7 1.0
C3' A:C102 4.5 31.5 0.7
O3B B:CTP101 4.6 36.8 0.8
O5' A:C102 4.6 36.0 0.7
P A:C102 4.7 39.8 0.7
NE2 E:HIS57 4.7 11.2 1.0
O E:HOH214 4.7 20.8 1.0
C A:HIS57 4.8 8.5 1.0
CA E:HIS57 4.8 11.9 1.0
O E:HOH203 5.0 19.9 1.0

Reference:

V.Murina, N.Lekontseva, A.Nikulin. Hfq Binds Ribonucleotides in Three Different Rna-Binding Sites. Acta Crystallogr.,Sect.D V. 69 1504 2013.
ISSN: ISSN 0907-4449
PubMed: 23897473
DOI: 10.1107/S090744491301010X
Page generated: Fri Aug 16 17:12:15 2024

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