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Calcium in PDB 4h19: Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop

Protein crystallography data

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop, PDB code: 4h19 was solved by M.W.Vetting, J.T.Bouvier, L.L.Morisco, S.R.Wasserman, S.Sojitra, 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) 197.84 / 1.80
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 178.363, 395.688, 177.802, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 17.5

Other elements in 4h19:

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms
Chlorine (Cl) 49 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop (pdb code 4h19). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop, PDB code: 4h19:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4h19

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Calcium binding site 1 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:26.2
occ:0.50
OD1 A:ASP268 2.4 14.6 1.0
NE2 A:HIS298 2.7 11.7 1.0
CE1 A:HIS298 3.1 11.5 1.0
CG A:ASP268 3.3 12.5 1.0
OD2 A:ASP268 3.5 17.2 1.0
CD2 A:HIS298 3.9 11.1 1.0
ND1 A:HIS298 4.4 13.8 1.0
CD1 A:LEU294 4.5 10.2 1.0
CB A:ASP268 4.6 10.8 1.0
CG A:HIS298 4.8 11.7 1.0
O A:HOH806 4.8 31.4 1.0
CG A:ARG264 4.9 10.4 1.0
CA A:ASP268 4.9 10.0 1.0

Calcium binding site 2 out of 10 in 4h19

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Calcium binding site 2 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:24.4
occ:1.00
OD1 C:ASP268 2.3 15.0 1.0
OD1 B:ASP268 2.4 15.2 1.0
NE2 B:HIS298 2.7 13.0 1.0
NE2 C:HIS298 2.8 11.1 1.0
CE1 B:HIS298 3.0 12.8 1.0
CE1 C:HIS298 3.1 11.7 1.0
CG B:ASP268 3.3 14.2 1.0
CG C:ASP268 3.3 14.4 1.0
OD2 C:ASP268 3.6 15.5 1.0
OD2 B:ASP268 3.6 14.9 1.0
CD2 B:HIS298 4.0 12.1 1.0
CD2 C:HIS298 4.1 11.1 1.0
ND1 B:HIS298 4.3 16.1 1.0
ND1 C:HIS298 4.4 13.6 1.0
CD1 C:LEU294 4.5 12.2 1.0
CD1 B:LEU294 4.5 12.0 1.0
CB B:ASP268 4.6 11.3 1.0
CB C:ASP268 4.6 12.1 1.0
CG B:HIS298 4.8 12.2 1.0
CG C:ARG264 4.9 12.6 1.0
O C:HOH742 4.9 27.5 1.0
CA B:ASP268 4.9 10.6 1.0
CG C:HIS298 4.9 11.2 1.0
CA C:ASP268 4.9 10.8 1.0
O B:HOH740 4.9 32.3 1.0
CG B:ARG264 5.0 11.9 1.0

Calcium binding site 3 out of 10 in 4h19

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Calcium binding site 3 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:21.4
occ:1.00
OD1 F:ASP268 2.3 14.7 1.0
OD1 D:ASP268 2.3 14.5 1.0
NE2 F:HIS298 2.7 11.2 1.0
NE2 D:HIS298 2.7 12.9 1.0
CE1 D:HIS298 3.1 13.8 1.0
CE1 F:HIS298 3.1 12.5 1.0
CG F:ASP268 3.2 14.9 1.0
CG D:ASP268 3.3 13.8 1.0
OD2 D:ASP268 3.5 18.7 1.0
OD2 F:ASP268 3.6 15.7 1.0
CD2 F:HIS298 4.0 11.2 1.0
CD2 D:HIS298 4.0 12.5 1.0
ND1 F:HIS298 4.4 13.8 1.0
ND1 D:HIS298 4.4 15.4 1.0
CD1 D:LEU294 4.4 10.1 1.0
CD1 F:LEU294 4.5 10.7 1.0
CB F:ASP268 4.6 12.3 1.0
CB D:ASP268 4.6 11.6 1.0
CA F:ASP268 4.8 11.7 1.0
CG F:HIS298 4.8 11.1 1.0
O F:HOH783 4.9 33.7 1.0
CG D:HIS298 4.9 11.6 1.0
O D:HOH760 4.9 26.4 1.0
CA D:ASP268 4.9 9.8 1.0
CG D:ARG264 4.9 11.5 1.0
CG F:ARG264 5.0 12.6 1.0

Calcium binding site 4 out of 10 in 4h19

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Calcium binding site 4 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:20.1
occ:1.00
OD1 G:ASP268 2.3 12.4 1.0
OD1 E:ASP268 2.3 16.5 1.0
NE2 E:HIS298 2.7 13.0 1.0
NE2 G:HIS298 2.7 13.3 1.0
CE1 E:HIS298 3.0 14.8 1.0
CE1 G:HIS298 3.2 13.8 1.0
CG G:ASP268 3.2 13.6 1.0
CG E:ASP268 3.3 14.9 1.0
OD2 G:ASP268 3.5 17.1 1.0
OD2 E:ASP268 3.5 17.3 1.0
CD2 E:HIS298 4.0 12.5 1.0
CD2 G:HIS298 4.0 14.5 1.0
ND1 E:HIS298 4.3 15.7 1.0
CD1 G:LEU294 4.4 9.5 1.0
ND1 G:HIS298 4.4 15.4 1.0
CD1 E:LEU294 4.5 13.1 1.0
CB G:ASP268 4.6 10.7 1.0
CB E:ASP268 4.6 12.4 1.0
CG E:HIS298 4.8 12.5 1.0
CA G:ASP268 4.9 9.3 1.0
CG G:ARG264 4.9 11.2 1.0
O G:HOH753 4.9 31.1 1.0
CG G:HIS298 4.9 12.3 1.0
CA E:ASP268 4.9 11.4 1.0
O E:HOH761 4.9 30.4 1.0
CG E:ARG264 5.0 11.3 1.0

Calcium binding site 5 out of 10 in 4h19

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Calcium binding site 5 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:23.5
occ:1.00
OD1 H:ASP268 2.4 15.9 1.0
OD1 I:ASP268 2.4 16.2 1.0
NE2 I:HIS298 2.7 13.1 1.0
NE2 H:HIS298 2.7 13.1 1.0
CE1 H:HIS298 3.1 14.3 1.0
CE1 I:HIS298 3.1 13.8 1.0
CG H:ASP268 3.3 14.6 1.0
CG I:ASP268 3.4 14.9 1.0
OD2 H:ASP268 3.6 14.9 1.0
OD2 I:ASP268 3.7 15.8 1.0
CD2 I:HIS298 4.0 12.7 1.0
CD2 H:HIS298 4.0 13.2 1.0
CD1 H:LEU294 4.3 12.1 1.0
ND1 H:HIS298 4.4 13.8 1.0
CD1 I:LEU294 4.4 10.8 1.0
ND1 I:HIS298 4.4 13.8 1.0
CB H:ASP268 4.6 11.8 1.0
CB I:ASP268 4.7 11.9 1.0
CG H:HIS298 4.9 12.6 1.0
CG I:HIS298 4.9 12.6 1.0
O H:HOH811 4.9 32.7 1.0
CG H:ARG264 4.9 13.2 1.0
CA I:ASP268 4.9 11.2 1.0
CA H:ASP268 4.9 11.4 1.0
O I:HOH797 4.9 29.5 1.0

Calcium binding site 6 out of 10 in 4h19

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Calcium binding site 6 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca401

b:22.8
occ:0.50
OD1 K:ASP268 2.4 16.6 1.0
NE2 K:HIS298 2.5 14.1 1.0
CE1 K:HIS298 2.9 14.4 1.0
CG K:ASP268 3.4 15.6 1.0
OD2 K:ASP268 3.8 16.8 1.0
CD2 K:HIS298 3.8 13.2 1.0
ND1 K:HIS298 4.2 14.7 1.0
CD1 K:LEU294 4.3 14.2 1.0
CG K:HIS298 4.6 12.3 1.0
CB K:ASP268 4.7 12.1 1.0
CA K:ASP268 4.8 11.5 1.0
CG2 K:ILE267 4.9 9.9 1.0

Calcium binding site 7 out of 10 in 4h19

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Calcium binding site 7 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca401

b:22.0
occ:1.00
OD1 M:ASP268 2.2 16.3 1.0
OD1 L:ASP268 2.3 17.1 1.0
NE2 L:HIS298 2.7 14.8 1.0
NE2 M:HIS298 2.7 14.6 1.0
CE1 L:HIS298 3.0 15.6 1.0
CE1 M:HIS298 3.1 16.2 1.0
CG M:ASP268 3.2 14.7 1.0
CG L:ASP268 3.3 15.7 1.0
OD2 M:ASP268 3.5 15.5 1.0
OD2 L:ASP268 3.6 15.7 1.0
CD2 M:HIS298 4.0 14.6 1.0
CD2 L:HIS298 4.0 14.5 1.0
ND1 L:HIS298 4.3 16.8 1.0
ND1 M:HIS298 4.4 18.7 1.0
CD1 M:LEU294 4.5 13.3 1.0
CD1 L:LEU294 4.5 12.3 1.0
CB M:ASP268 4.6 13.2 1.0
CB L:ASP268 4.6 12.8 1.0
O M:HOH711 4.7 29.6 1.0
O L:HOH740 4.8 36.8 1.0
CG L:HIS298 4.8 13.1 1.0
CA M:ASP268 4.9 11.5 1.0
CG M:HIS298 4.9 14.7 1.0
CA L:ASP268 4.9 11.6 1.0
CG L:ARG264 4.9 12.0 1.0
CG M:ARG264 4.9 13.6 1.0

Calcium binding site 8 out of 10 in 4h19

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Calcium binding site 8 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca401

b:20.4
occ:1.00
OD1 P:ASP268 2.2 14.4 1.0
OD1 N:ASP268 2.3 14.9 1.0
NE2 N:HIS298 2.6 15.2 1.0
NE2 P:HIS298 2.7 13.3 1.0
CE1 N:HIS298 3.0 16.1 1.0
CE1 P:HIS298 3.1 14.1 1.0
CG P:ASP268 3.1 13.9 1.0
CG N:ASP268 3.2 13.7 1.0
OD2 P:ASP268 3.4 15.9 1.0
OD2 N:ASP268 3.4 15.9 1.0
CD2 N:HIS298 4.0 14.2 1.0
CD2 P:HIS298 4.0 13.7 1.0
ND1 N:HIS298 4.3 17.5 1.0
ND1 P:HIS298 4.4 14.2 1.0
CD1 N:LEU294 4.4 12.1 1.0
CD1 P:LEU294 4.4 13.1 1.0
CB P:ASP268 4.5 12.1 1.0
CB N:ASP268 4.6 11.4 1.0
CG N:HIS298 4.8 13.2 1.0
O P:HOH683 4.8 30.9 1.0
O N:HOH754 4.8 34.0 1.0
CG P:HIS298 4.9 12.3 1.0
CA P:ASP268 4.9 11.0 1.0
CA N:ASP268 4.9 10.7 1.0
CG P:ARG264 4.9 12.6 1.0
CG N:ARG264 4.9 12.5 1.0

Calcium binding site 9 out of 10 in 4h19

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Calcium binding site 9 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:21.5
occ:0.50
OD1 J:ASP268 2.3 14.8 1.0
NE2 J:HIS298 2.5 11.6 1.0
CE1 J:HIS298 2.9 11.5 1.0
CG J:ASP268 3.3 13.8 1.0
OD2 J:ASP268 3.8 14.3 1.0
CD2 J:HIS298 3.8 11.1 1.0
ND1 J:HIS298 4.2 12.9 1.0
CD1 J:LEU294 4.4 12.1 1.0
CB J:ASP268 4.6 11.2 1.0
CG J:HIS298 4.7 11.4 1.0
CA J:ASP268 4.8 10.6 1.0
CG2 J:ILE267 4.9 10.8 1.0

Calcium binding site 10 out of 10 in 4h19

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Calcium binding site 10 out of 10 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D- Ribonohydroxamate, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca401

b:22.3
occ:0.50
OD1 O:ASP268 2.3 14.3 1.0
NE2 O:HIS298 2.5 12.1 1.0
CE1 O:HIS298 2.8 13.2 1.0
CG O:ASP268 3.3 14.0 1.0
OD2 O:ASP268 3.6 17.0 1.0
CD2 O:HIS298 3.8 11.9 1.0
ND1 O:HIS298 4.1 14.0 1.0
CD1 O:LEU294 4.4 12.3 1.0
CB O:ASP268 4.6 12.0 1.0
CG O:HIS298 4.6 11.6 1.0
CA O:ASP268 4.9 11.8 1.0
O O:HOH772 5.0 32.3 1.0

Reference:

M.W.Vetting, J.T.Bouvier, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Enolase (Mandelate Racemase Subgroup, Target Efi-502087) From Agrobacterium Tumefaciens, with Bound Mg and D-Ribonohydroxamate, Ordered Loop To Be Published.
Page generated: Sat Dec 12 04:49:39 2020

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