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Magnesium in PDB 3ugv: Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg

Protein crystallography data

The structure of Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg, PDB code: 3ugv was solved by M.W.Vetting, R.Toro, R.Bhosle, S.R.Wasserman, L.L.Morisco, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative(Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 114.64 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.711, 152.984, 173.535, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.8

Other elements in 3ugv:

The structure of Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg (pdb code 3ugv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg, PDB code: 3ugv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 3ugv

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Magnesium binding site 1 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:38.2
occ:1.00
 OE2 A:GLU228 2.1 35.4 1.0
O A:HOH411 2.1 29.1 1.0
O A:HOH429 2.1 40.9 1.0
O A:HOH394 2.2 23.5 1.0
OE1 A:GLU254 2.2 43.0 1.0
OD2 A:ASP202 2.3 26.8 1.0
CD A:GLU254 3.2 39.5 1.0
CD A:GLU228 3.2 28.2 1.0
OE2 A:GLU254 3.5 32.0 1.0
CG A:ASP202 3.5 28.3 1.0
NZ A:LYS171 3.5 26.1 1.0
O A:HOH445 3.8 36.2 1.0
O A:HOH473 3.9 34.0 1.0
OE1 A:GLU228 4.0 23.5 1.0
OD1 A:ASP202 4.1 26.7 1.0
CD2 A:HIS304 4.1 27.8 1.0
NE2 A:HIS304 4.2 28.2 1.0
CE A:MET275 4.2 21.6 1.0
CG A:GLU228 4.3 17.0 1.0
OD1 A:ASN204 4.5 47.9 1.0
CE A:LYS171 4.5 30.1 1.0
CG A:GLU254 4.5 29.3 1.0
CB A:ASP202 4.6 23.4 1.0
OE1 A:GLU324 4.7 32.2 1.0
O A:HOH397 4.7 25.9 1.0
CD A:LYS171 4.8 27.5 1.0
OE1 A:GLU229 4.9 55.7 1.0
SD A:MET275 5.0 25.1 1.0

Magnesium binding site 2 out of 16 in 3ugv

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Magnesium binding site 2 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:21.1
occ:1.00
 O A:HOH375 2.0 20.0 1.0
O D:HOH371 2.0 14.1 1.0
O A:HOH382 2.0 20.3 1.0
O A:HOH370 2.1 13.6 1.0
O A:ARG243 2.1 16.4 1.0
O A:LEU246 2.1 27.3 1.0
C A:LEU246 3.2 31.5 1.0
C A:ARG243 3.3 26.1 1.0
OD1 A:ASP272 4.0 27.7 1.0
CA A:ARG243 4.1 24.5 1.0
N A:LYS247 4.1 22.6 1.0
CA A:LEU246 4.2 28.5 1.0
OD2 D:ASP245 4.2 37.2 1.0
CA A:LYS247 4.2 21.4 1.0
O A:LYS247 4.2 25.8 1.0
OD2 A:ASP272 4.2 24.5 1.0
O A:HIS244 4.2 27.7 1.0
N A:HIS244 4.3 23.4 1.0
O A:THR248 4.3 19.8 1.0
C A:LYS247 4.3 22.9 1.0
N A:LEU246 4.3 26.5 1.0
CG A:ARG243 4.3 26.6 1.0
CB A:LEU246 4.4 18.4 1.0
C A:HIS244 4.4 22.8 1.0
CA A:HIS244 4.4 24.7 1.0
CG A:ASP272 4.5 30.2 1.0
OD1 D:ASP245 4.6 42.2 1.0
CB A:ARG243 4.8 24.2 1.0
CG D:ASP245 4.8 33.4 1.0
CE D:MET213 4.8 23.2 1.0
O A:LEU242 4.9 29.5 1.0

Magnesium binding site 3 out of 16 in 3ugv

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Magnesium binding site 3 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:34.4
occ:1.00
 O B:HOH866 2.0 34.3 1.0
OE1 B:GLU254 2.0 46.0 1.0
O B:HOH486 2.1 32.6 1.0
OE2 B:GLU228 2.1 46.8 1.0
O B:HOH407 2.1 36.9 1.0
OD2 B:ASP202 2.2 31.6 1.0
CD B:GLU254 3.1 38.7 1.0
CD B:GLU228 3.2 48.1 1.0
CG B:ASP202 3.2 29.7 1.0
OE2 B:GLU254 3.4 44.9 1.0
OD1 B:ASP202 3.5 25.4 1.0
CG B:GLU228 3.9 41.8 1.0
NZ B:LYS171 4.0 46.6 1.0
OE1 B:GLU228 4.1 51.8 1.0
OD1 B:ASN204 4.1 52.3 1.0
O B:HOH539 4.1 36.0 1.0
O B:HOH398 4.3 33.1 1.0
CG B:GLU254 4.4 37.3 1.0
OE1 B:GLU229 4.4 64.3 1.0
NE2 B:HIS304 4.4 35.7 1.0
CB B:ASP202 4.5 23.5 1.0
CD2 B:HIS304 4.6 28.8 1.0
CE B:MET275 4.6 29.9 1.0
CE B:LYS171 4.9 41.5 1.0
O B:HOH815 5.0 47.6 1.0
CG B:ASN204 5.0 41.9 1.0

Magnesium binding site 4 out of 16 in 3ugv

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Magnesium binding site 4 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:26.0
occ:1.00
 O B:LEU246 2.0 25.4 1.0
O B:HOH381 2.0 24.7 1.0
O B:ARG243 2.0 25.2 1.0
O B:HOH369 2.0 18.8 1.0
O B:HOH370 2.1 20.2 1.0
O A:HOH374 2.1 16.2 1.0
C B:LEU246 3.2 28.3 1.0
C B:ARG243 3.2 29.8 1.0
OD1 B:ASP272 4.0 25.7 1.0
CA B:ARG243 4.1 30.1 1.0
CA B:LEU246 4.1 21.6 1.0
N B:LEU246 4.1 22.9 1.0
N B:LYS247 4.2 22.8 1.0
N B:HIS244 4.2 27.1 1.0
CA B:LYS247 4.3 30.9 1.0
O B:HIS244 4.3 27.2 1.0
OD2 A:ASP245 4.3 36.4 1.0
CB B:LEU246 4.3 21.7 1.0
OD1 A:ASP245 4.3 32.9 1.0
CA B:HIS244 4.4 29.0 1.0
C B:HIS244 4.4 27.9 1.0
OD2 B:ASP272 4.4 29.0 1.0
CG B:ARG243 4.4 28.8 1.0
O B:THR248 4.5 26.4 1.0
C B:LYS247 4.5 34.5 1.0
O B:LYS247 4.6 31.7 1.0
CG B:ASP272 4.6 31.0 1.0
CG A:ASP245 4.7 37.0 1.0
CB B:ARG243 4.8 30.3 1.0
O B:LEU242 4.9 28.5 1.0
CD B:ARG243 5.0 34.7 1.0

Magnesium binding site 5 out of 16 in 3ugv

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Magnesium binding site 5 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg500

b:37.7
occ:1.00
 OE2 C:GLU228 2.0 35.0 1.0
O C:HOH707 2.1 32.4 1.0
O C:HOH782 2.1 40.9 1.0
O C:HOH667 2.1 43.2 1.0
OD2 C:ASP202 2.2 37.8 1.0
OE1 C:GLU254 2.2 35.9 1.0
CD C:GLU228 3.0 37.3 1.0
CG C:ASP202 3.1 35.4 1.0
CD C:GLU254 3.2 36.8 1.0
OD1 C:ASP202 3.5 32.6 1.0
OE2 C:GLU254 3.6 45.1 1.0
CG C:GLU228 3.7 26.8 1.0
OE1 C:GLU228 3.8 42.8 1.0
O C:HOH584 4.1 38.9 1.0
NZ C:LYS171 4.1 39.2 1.0
OD1 C:ASN204 4.2 46.9 1.0
O C:HOH372 4.2 24.1 1.0
OE1 C:GLU229 4.4 50.5 1.0
CE C:MET275 4.4 34.1 1.0
CB C:ASP202 4.5 32.0 1.0
CG C:GLU254 4.5 22.6 1.0
NE2 C:HIS304 4.6 37.0 1.0
CD2 C:HIS304 4.6 35.7 1.0
O C:HOH775 4.6 44.8 1.0
CB C:GLU228 4.9 28.8 1.0
CE C:LYS171 5.0 36.6 1.0
SD C:MET275 5.0 31.1 1.0
CG C:ASN204 5.0 41.0 1.0

Magnesium binding site 6 out of 16 in 3ugv

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Magnesium binding site 6 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:22.8
occ:1.00
 O C:ARG243 2.0 23.1 1.0
O B:HOH380 2.1 28.9 1.0
O C:LEU246 2.1 28.2 1.0
O C:HOH378 2.1 26.4 1.0
O C:HOH370 2.1 20.6 1.0
O B:HOH373 2.1 24.3 1.0
C C:ARG243 3.2 27.6 1.0
C C:LEU246 3.3 29.7 1.0
CA C:ARG243 4.0 26.6 1.0
OD1 C:ASP272 4.1 29.0 1.0
CG C:ARG243 4.1 25.7 1.0
N C:HIS244 4.2 23.6 1.0
CA C:LEU246 4.2 23.3 1.0
N C:LYS247 4.2 27.1 1.0
OD2 B:ASP245 4.2 44.3 1.0
CA C:LYS247 4.3 28.0 1.0
OD2 C:ASP272 4.3 30.7 1.0
N C:LEU246 4.3 17.4 1.0
O C:THR248 4.3 24.6 1.0
O C:HIS244 4.3 23.2 1.0
CA C:HIS244 4.4 22.7 1.0
OD1 B:ASP245 4.4 50.6 1.0
C C:HIS244 4.4 25.7 1.0
CB C:LEU246 4.5 23.8 1.0
C C:LYS247 4.5 25.4 1.0
O C:LYS247 4.6 32.8 1.0
CG C:ASP272 4.6 32.6 1.0
CB C:ARG243 4.6 23.0 1.0
CG B:ASP245 4.7 44.7 1.0
O C:LEU242 4.8 31.7 1.0

Magnesium binding site 7 out of 16 in 3ugv

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Magnesium binding site 7 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg500

b:28.6
occ:1.00
 OE2 D:GLU228 2.0 29.0 1.0
O D:HOH381 2.1 18.4 1.0
OD2 D:ASP202 2.1 26.2 1.0
O D:HOH415 2.1 27.2 1.0
O D:HOH401 2.1 25.3 1.0
OE1 D:GLU254 2.2 32.8 1.0
CD D:GLU254 3.1 37.1 1.0
CD D:GLU228 3.1 29.5 1.0
CG D:ASP202 3.2 26.1 1.0
OE2 D:GLU254 3.3 44.6 1.0
OD1 D:ASP202 3.6 23.6 1.0
O D:HOH378 3.9 17.1 1.0
NZ D:LYS171 3.9 33.8 1.0
OE1 D:GLU228 3.9 22.2 1.0
CG D:GLU228 4.0 17.3 1.0
OD1 D:ASN204 4.2 36.5 1.0
OE1 D:GLU229 4.3 42.6 1.0
O D:HOH763 4.4 43.9 1.0
NE2 D:HIS304 4.4 20.1 1.0
O D:HOH399 4.4 25.1 1.0
CD2 D:HIS304 4.4 17.7 1.0
CE D:MET275 4.4 27.8 1.0
CG D:GLU254 4.4 17.4 1.0
CB D:ASP202 4.5 19.1 1.0
CE D:LYS171 4.8 30.1 1.0
CG D:ASN204 4.9 31.3 1.0
O D:HOH435 5.0 30.0 1.0

Magnesium binding site 8 out of 16 in 3ugv

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Magnesium binding site 8 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


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 An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:19.4
occ:1.00
 O D:LEU246 2.1 24.5 1.0
O D:HOH372 2.1 16.3 1.0
O D:ARG243 2.1 18.5 1.0
O C:HOH369 2.1 19.5 1.0
O D:HOH369 2.1 13.4 1.0
O C:HOH368 2.1 16.5 1.0
C D:ARG243 3.3 20.6 1.0
C D:LEU246 3.3 18.8 1.0
CG D:ARG243 4.0 23.5 1.0
OD1 D:ASP272 4.0 22.3 1.0
CA D:ARG243 4.0 20.0 1.0
OD1 C:ASP245 4.2 43.2 1.0
N D:LYS247 4.2 14.8 1.0
OD2 D:ASP272 4.2 25.9 1.0
CA D:LYS247 4.2 17.1 1.0
CA D:LEU246 4.2 18.0 1.0
N D:HIS244 4.3 19.9 1.0
N D:LEU246 4.3 15.2 1.0
O D:HIS244 4.3 25.0 1.0
OD2 C:ASP245 4.4 38.9 1.0
C D:HIS244 4.4 22.0 1.0
CA D:HIS244 4.4 14.1 1.0
C D:LYS247 4.5 24.6 1.0
O D:THR248 4.5 14.1 1.0
CG D:ASP272 4.5 25.9 1.0
CB D:LEU246 4.5 15.7 1.0
O D:LYS247 4.6 34.2 1.0
CB D:ARG243 4.6 15.0 1.0
CG C:ASP245 4.7 37.2 1.0
CE C:MET213 4.9 24.7 1.0

Magnesium binding site 9 out of 16 in 3ugv

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Magnesium binding site 9 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg500

b:42.6
occ:1.00
 O E:HOH836 2.0 45.8 1.0
OE2 E:GLU228 2.1 40.3 1.0
O E:HOH726 2.1 44.4 1.0
O E:HOH386 2.1 32.6 1.0
OD2 E:ASP202 2.1 36.9 1.0
OE1 E:GLU254 2.1 33.3 1.0
CD E:GLU254 3.1 37.5 1.0
CD E:GLU228 3.2 38.3 1.0
CG E:ASP202 3.3 36.6 1.0
OE2 E:GLU254 3.3 42.2 1.0
O E:HOH582 3.7 39.2 1.0
OD1 E:ASP202 3.8 40.6 1.0
NZ E:LYS171 3.9 39.7 1.0
OE1 E:GLU228 4.0 27.9 1.0
OD1 E:ASN204 4.0 29.4 1.0
NE2 E:HIS304 4.2 34.0 1.0
CG E:GLU228 4.3 26.5 1.0
CE E:MET275 4.3 29.7 1.0
O E:HOH835 4.4 49.7 1.0
CD2 E:HIS304 4.4 29.5 1.0
CG E:GLU254 4.5 31.5 1.0
CB E:ASP202 4.5 31.3 1.0
O E:HOH525 4.5 37.0 1.0
O E:HOH368 4.7 33.4 1.0
OE1 E:GLU229 4.9 56.9 1.0
CG E:ASN204 4.9 30.2 1.0
OE1 E:GLU324 4.9 56.9 1.0
CE E:LYS171 4.9 37.6 1.0

Magnesium binding site 10 out of 16 in 3ugv

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Magnesium binding site 10 out of 16 in the Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:23.1
occ:1.00
 O E:HOH370 2.0 20.3 1.0
O H:HOH446 2.0 35.9 1.0
O H:HOH370 2.1 20.9 1.0
O E:HOH371 2.1 21.8 1.0
O E:LEU246 2.1 31.0 1.0
O E:ARG243 2.2 19.7 1.0
C E:LEU246 3.3 24.1 1.0
C E:ARG243 3.4 25.2 1.0
O H:HOH711 4.1 43.4 1.0
CA E:LYS247 4.1 31.5 1.0
OD1 H:ASP245 4.2 45.4 1.0
N E:LYS247 4.2 23.7 1.0
OD2 E:ASP272 4.2 28.6 1.0
CA E:ARG243 4.2 26.0 1.0
OD1 E:ASP272 4.2 27.0 1.0
CG E:ARG243 4.3 28.7 1.0
O E:HIS244 4.3 30.0 1.0
O E:LYS247 4.3 29.7 1.0
CA E:LEU246 4.3 21.7 1.0
OD2 H:ASP245 4.3 52.9 1.0
C E:LYS247 4.4 23.8 1.0
O E:THR248 4.4 24.7 1.0
N E:HIS244 4.4 18.8 1.0
N E:LEU246 4.5 21.7 1.0
C E:HIS244 4.5 21.4 1.0
CA E:HIS244 4.6 21.7 1.0
CB E:LEU246 4.6 24.5 1.0
CG H:ASP245 4.6 42.9 1.0
CG E:ASP272 4.6 22.3 1.0
CB E:ARG243 4.9 30.6 1.0
CE H:MET213 4.9 29.3 1.0

Reference:

M.W.Vetting, R.Toro, R.Bhosle, S.R.Wasserman, L.L.Morisco, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Enolase From Alpha Pretobacterium BAL199 (Efi Target Efi-501650) with Bound Mg To Be Published.
Page generated: Thu Aug 15 12:30:58 2024

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