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Magnesium in PDB 4p9d: Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.

Protein crystallography data

The structure of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp., PDB code: 4p9d was solved by A.Marx, A.Alian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.02 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.900, 79.020, 126.520, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.8

Other elements in 4p9d:

The structure of Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. (pdb code 4p9d). 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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp., PDB code: 4p9d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4p9d

Go back to Magnesium Binding Sites List in 4p9d
Magnesium binding site 1 out of 6 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:37.3
occ:1.00
 O A:HOH301 2.1 25.6 1.0
OD1 A:ASN52 2.1 43.1 1.0
O3A A:TTP203 2.1 29.1 1.0
O A:HOH305 2.1 30.0 1.0
O2B A:TTP203 2.2 34.8 1.0
O3G A:TTP203 2.3 26.3 1.0
PB A:TTP203 2.7 32.0 1.0
CG A:ASN52 3.2 40.5 1.0
PG A:TTP203 3.4 32.3 1.0
PA A:TTP203 3.5 28.0 1.0
O3B A:TTP203 3.5 30.0 1.0
ND2 A:ASN52 3.7 37.9 1.0
O A:PRO46 3.9 29.3 1.0
O1B A:TTP203 3.9 28.1 1.0
N A:GLY48 4.0 29.7 1.0
O A:PHE49 4.0 33.3 1.0
O2G A:TTP203 4.0 32.2 1.0
OG1 A:THR45 4.0 30.3 1.0
N A:PHE49 4.1 30.9 1.0
O1A A:TTP203 4.3 30.6 1.0
C5' A:TTP203 4.4 29.6 1.0
O2A A:TTP203 4.4 30.7 1.0
CB A:ASN52 4.5 40.7 1.0
O5' A:TTP203 4.5 28.2 1.0
CA A:GLY48 4.6 30.1 1.0
O1G A:TTP203 4.7 28.6 1.0
C A:GLY48 4.7 30.6 1.0
CA A:ASN52 4.7 41.4 1.0
CA A:SER47 4.8 29.3 1.0
C A:SER47 4.8 29.5 1.0
O A:THR51 4.8 39.3 1.0
C A:PHE49 4.8 33.2 1.0
CB A:PHE49 4.8 31.5 1.0
CA A:PHE49 4.8 31.8 1.0
C A:PRO46 4.9 28.6 1.0

Magnesium binding site 2 out of 6 in 4p9d

Go back to Magnesium Binding Sites List in 4p9d
Magnesium binding site 2 out of 6 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:32.0
occ:1.00
 OD1 B:ASN52 2.1 48.7 1.0
O2B B:TTP204 2.1 34.7 1.0
O2G B:TTP204 2.2 37.5 1.0
O B:HOH306 2.2 30.0 1.0
O2A B:TTP204 2.3 28.1 1.0
PA B:TTP204 2.6 32.3 1.0
CG B:ASN52 3.1 45.9 1.0
PB B:TTP204 3.3 34.2 1.0
O3A B:TTP204 3.4 33.3 1.0
ND2 B:ASN52 3.5 46.0 1.0
PG B:TTP204 3.5 41.2 1.0
O5' B:TTP204 3.6 29.5 1.0
O B:PRO46 3.7 37.0 1.0
C5' B:TTP204 3.8 30.8 1.0
O3B B:TTP204 3.9 36.1 1.0
O1A B:TTP204 4.0 28.0 1.0
OG1 B:THR45 4.2 33.0 1.0
O3G B:TTP204 4.3 39.8 1.0
CB B:ASN52 4.3 45.3 1.0
N B:GLY48 4.4 39.6 1.0
O B:PHE49 4.5 41.0 1.0
O B:THR51 4.5 45.6 1.0
O1G B:TTP204 4.6 39.6 1.0
O1B B:TTP204 4.6 36.2 1.0
CA B:ASN52 4.6 45.8 1.0
CA B:SER47 4.6 38.4 1.0
O B:THR45 4.7 33.0 1.0
C B:PRO46 4.7 36.9 1.0
N B:PHE49 4.7 40.1 1.0
C B:SER47 4.9 39.0 1.0

Magnesium binding site 3 out of 6 in 4p9d

Go back to Magnesium Binding Sites List in 4p9d
Magnesium binding site 3 out of 6 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:18.6
occ:1.00
 OD1 C:ASN52 2.0 40.8 1.0
O2B C:TTP203 2.1 31.4 1.0
O1G C:TTP203 2.1 36.1 1.0
O2A C:TTP203 2.3 30.7 1.0
PA C:TTP203 2.6 31.0 1.0
CG C:ASN52 3.0 39.6 1.0
PB C:TTP203 3.2 28.9 1.0
O3A C:TTP203 3.3 28.8 1.0
PG C:TTP203 3.5 38.7 1.0
ND2 C:ASN52 3.5 41.8 1.0
O5' C:TTP203 3.6 32.1 1.0
O3B C:TTP203 3.8 32.4 1.0
O C:PRO46 3.9 24.5 1.0
O1A C:TTP203 3.9 32.3 1.0
C5' C:TTP203 4.1 29.9 1.0
OG1 C:THR45 4.2 23.3 1.0
O3G C:TTP203 4.4 36.7 1.0
N C:GLY48 4.4 29.5 1.0
CB C:ASN52 4.4 38.2 1.0
O2G C:TTP203 4.4 37.1 1.0
O1B C:TTP203 4.5 29.8 1.0
CA C:SER47 4.8 27.6 1.0
CA C:ASN52 4.8 38.3 1.0
C C:PRO46 4.8 25.1 1.0
O C:THR45 4.9 23.2 1.0
N C:PHE49 4.9 32.8 1.0
O C:PHE49 5.0 34.9 1.0

Magnesium binding site 4 out of 6 in 4p9d

Go back to Magnesium Binding Sites List in 4p9d
Magnesium binding site 4 out of 6 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:45.6
occ:1.00
 OD1 D:ASN52 2.1 49.8 1.0
O2B D:TTP203 2.2 44.4 1.0
O2A D:TTP203 2.5 38.0 1.0
PA D:TTP203 2.6 39.0 1.0
O D:HOH305 2.7 30.0 1.0
PB D:TTP203 3.0 43.4 1.0
O3B D:TTP203 3.1 46.9 1.0
CG D:ASN52 3.2 48.5 1.0
O3A D:TTP203 3.2 41.6 1.0
O5' D:TTP203 3.6 38.2 1.0
OG1 D:THR45 3.8 35.2 1.0
O D:PRO46 3.9 35.5 1.0
ND2 D:ASN52 4.0 46.5 1.0
O1A D:TTP203 4.0 39.1 1.0
C5' D:TTP203 4.0 37.1 1.0
O1G D:TTP203 4.2 52.0 1.0
PG D:TTP203 4.2 52.2 1.0
CB D:ASN52 4.3 48.7 1.0
O1B D:TTP203 4.4 38.3 1.0
N D:GLY48 4.5 37.6 1.0
CA D:ASN52 4.5 49.0 1.0
O D:THR45 4.6 34.8 1.0
O D:THR51 4.7 47.2 1.0
CA D:SER47 4.8 36.4 1.0
N D:PHE49 4.8 40.0 1.0
C D:PRO46 4.8 35.4 1.0
O2G D:TTP203 4.8 51.9 1.0
O D:PHE49 4.9 42.9 1.0

Magnesium binding site 5 out of 6 in 4p9d

Go back to Magnesium Binding Sites List in 4p9d
Magnesium binding site 5 out of 6 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:51.7
occ:1.00
 O2G E:TTP203 2.0 54.9 1.0
OD1 E:ASN52 2.1 61.6 1.0
O E:HOH302 2.2 30.4 1.0
O2B E:TTP203 2.2 52.6 1.0
O2A E:TTP203 2.7 50.6 1.0
PA E:TTP203 2.9 51.0 1.0
CG E:ASN52 3.0 62.6 1.0
ND2 E:ASN52 3.4 62.1 1.0
PB E:TTP203 3.4 51.9 1.0
O E:PRO46 3.4 43.5 1.0
PG E:TTP203 3.4 55.8 1.0
O3A E:TTP203 3.7 51.3 1.0
O5' E:TTP203 3.8 47.0 1.0
O3B E:TTP203 3.9 53.5 1.0
OG1 E:THR45 4.1 40.5 1.0
C5' E:TTP203 4.1 43.5 1.0
O1G E:TTP203 4.2 53.1 1.0
N E:GLY48 4.3 50.0 1.0
O E:THR45 4.3 41.5 1.0
O E:PHE49 4.3 57.1 1.0
O1A E:TTP203 4.3 48.7 1.0
N E:PHE49 4.3 55.2 1.0
CB E:ASN52 4.4 62.9 1.0
O3G E:TTP203 4.4 56.0 1.0
C E:PRO46 4.5 44.1 1.0
CA E:SER47 4.6 47.2 1.0
CB E:PHE49 4.6 56.0 1.0
O1B E:TTP203 4.7 52.5 1.0
C E:SER47 4.8 48.4 1.0
CA E:ASN52 4.8 63.3 1.0
O E:THR51 4.9 62.6 1.0
CA E:PHE49 4.9 56.2 1.0
C E:PHE49 5.0 57.2 1.0
N E:SER47 5.0 45.6 1.0

Magnesium binding site 6 out of 6 in 4p9d

Go back to Magnesium Binding Sites List in 4p9d
Magnesium binding site 6 out of 6 in the Crystal Structure of Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp.


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 Dcmp Deaminase From the Cyanophage S-TIM5 in Complex with Dtmp and Dttp. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:15.5
occ:1.00
 O3G F:TTP203 2.0 36.7 1.0
O F:HOH301 2.1 13.8 1.0
OD1 F:ASN52 2.1 42.0 1.0
O2B F:TTP203 2.1 38.9 1.0
O2A F:TTP203 2.3 34.8 1.0
PA F:TTP203 2.4 35.8 1.0
CG F:ASN52 3.0 41.2 1.0
PB F:TTP203 3.0 35.1 1.0
O3A F:TTP203 3.1 36.0 1.0
PG F:TTP203 3.3 37.8 1.0
ND2 F:ASN52 3.3 40.8 1.0
O5' F:TTP203 3.5 36.0 1.0
O3B F:TTP203 3.5 36.0 1.0
O1A F:TTP203 3.8 36.9 1.0
O2G F:TTP203 4.1 34.5 1.0
O F:PRO46 4.1 35.3 1.0
N F:GLY48 4.2 37.8 1.0
O1G F:TTP203 4.3 35.3 1.0
OG1 F:THR45 4.4 33.8 1.0
CB F:ASN52 4.4 40.8 1.0
O1B F:TTP203 4.4 36.3 1.0
C5' F:TTP203 4.4 35.5 1.0
N F:PHE49 4.6 39.8 1.0
O F:PHE49 4.7 39.0 1.0
CA F:SER47 4.8 35.8 1.0
CA F:GLY48 4.9 38.9 1.0
CA F:ASN52 4.9 40.9 1.0
C F:SER47 5.0 36.7 1.0

Reference:

A.Marx, A.Alian. The First Crystal Structure of A Dttp Bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.617720
Page generated: Tue Aug 20 01:15:33 2024

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