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Calcium in PDB 4ln1: Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452

Enzymatic activity of Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452

All present enzymatic activity of Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452, PDB code: 4ln1 was solved by V.N.Malashkevich, J.B.Bonanno, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garforth, A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.Lim, A.Celikgil, G.Villegas, B.Evans, J.Love, A.Fiser, K.Khafizov, R.Seidel, S.C.Almo, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.98 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.719, 75.453, 100.145, 90.00, 89.99, 90.00
R / Rfree (%) 20.9 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 (pdb code 4ln1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452, PDB code: 4ln1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ln1

Go back to Calcium Binding Sites List in 4ln1
Calcium binding site 1 out of 6 in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452


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 L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:34.5
occ:1.00
 O C:HOH649 2.3 46.7 1.0
O C:HOH648 2.4 38.0 1.0
O A:HOH650 2.5 27.9 1.0
O A:HOH686 2.5 53.2 1.0
O C:HOH622 2.5 31.2 1.0
O A:HOH684 2.5 40.4 1.0
O C:HOH632 2.6 36.4 1.0
O A:HOH624 2.7 30.6 1.0
ND2 A:ASN249 4.0 22.0 1.0
O C:VAL29 4.1 25.5 1.0
ND2 C:ASN249 4.2 31.4 1.0
O A:HOH617 4.3 38.0 1.0
OE2 C:GLU31 4.3 28.0 1.0
ND2 C:ASN6 4.4 31.4 1.0
O A:VAL29 4.5 28.2 1.0
OE2 A:GLU31 4.6 27.1 1.0
O C:HOH629 4.7 37.5 1.0
ND2 A:ASN6 4.7 33.2 1.0
O C:HOH639 4.8 40.6 1.0
O A:HOH629 4.9 36.7 1.0
O C:HOH608 4.9 38.1 1.0
CG A:ASN249 5.0 22.6 1.0

Calcium binding site 2 out of 6 in 4ln1

Go back to Calcium Binding Sites List in 4ln1
Calcium binding site 2 out of 6 in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452


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 L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:37.4
occ:1.00
 O A:HOH672 2.3 38.3 1.0
O A:HOH688 2.4 41.7 1.0
O A:HOH654 2.5 45.4 1.0
O A:ILE5 2.5 31.8 1.0
O A:LYS3 2.5 39.8 1.0
OD2 A:ASP75 2.6 30.4 1.0
O A:HOH689 2.6 42.8 1.0
OD1 A:ASP75 2.7 34.7 1.0
CG A:ASP75 3.0 31.9 1.0
C A:LYS3 3.5 40.5 1.0
C A:ILE5 3.7 31.0 1.0
CA A:LYS3 4.0 42.1 1.0
O A:ASP73 4.0 38.5 1.0
O A:LYS2 4.2 45.1 1.0
N A:ILE5 4.3 34.1 1.0
NH2 A:ARG280 4.4 34.2 0.5
CA A:ASN6 4.4 30.5 1.0
N A:ASN6 4.5 30.4 1.0
CB A:ASP75 4.5 31.5 1.0
N A:GLY4 4.6 39.8 1.0
CA A:ILE5 4.6 32.1 1.0
O A:HOH630 4.7 46.2 1.0
N A:ARG7 4.7 28.7 1.0
OD1 A:ASN6 4.8 36.3 1.0
NH1 A:ARG280 4.8 33.8 0.5
CB A:LYS3 4.9 43.9 1.0
C A:GLY4 5.0 38.6 1.0
N A:LYS3 5.0 44.3 1.0
N A:ASP75 5.0 32.7 1.0
C A:LYS2 5.0 46.2 1.0

Calcium binding site 3 out of 6 in 4ln1

Go back to Calcium Binding Sites List in 4ln1
Calcium binding site 3 out of 6 in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452


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 L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:34.8
occ:1.00
 O D:HOH662 2.3 40.3 1.0
O B:HOH643 2.4 27.4 1.0
O D:HOH642 2.5 29.7 1.0
O B:HOH627 2.6 33.1 1.0
O D:HOH627 2.7 33.2 1.0
OD1 B:ASN249 4.0 26.2 1.0
ND2 D:ASN249 4.1 31.9 1.0
O D:VAL29 4.2 25.0 1.0
O B:HOH677 4.4 43.9 1.0
OE2 D:GLU31 4.4 27.2 1.0
O B:VAL29 4.5 27.5 1.0
ND2 D:ASN6 4.6 33.6 1.0
O D:HOH625 4.7 33.0 1.0
OE2 B:GLU31 4.7 27.3 1.0
O B:HOH652 4.8 37.5 1.0
CG B:ASN249 4.9 25.5 1.0
O B:HOH679 4.9 45.9 1.0
O D:HOH618 4.9 40.0 1.0

Calcium binding site 4 out of 6 in 4ln1

Go back to Calcium Binding Sites List in 4ln1
Calcium binding site 4 out of 6 in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452


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 L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:40.9
occ:1.00
 O B:HOH650 2.1 41.3 1.0
O B:ILE5 2.4 30.1 1.0
O B:HOH657 2.6 47.5 1.0
OD2 B:ASP75 2.6 36.0 1.0
O B:LYS3 2.7 44.6 1.0
OD1 B:ASP75 2.8 36.7 1.0
CG B:ASP75 3.1 35.1 1.0
C B:LYS3 3.5 43.9 1.0
C B:ILE5 3.6 29.8 1.0
CA B:LYS3 3.8 46.1 1.0
O B:LYS2 3.9 50.9 1.0
O B:ASP73 4.0 41.3 1.0
N B:ILE5 4.2 33.5 1.0
CA B:ASN6 4.4 28.5 1.0
N B:ASN6 4.4 29.2 1.0
CB B:ASP75 4.6 33.0 1.0
CA B:ILE5 4.6 31.4 1.0
O B:HOH645 4.6 48.8 1.0
OD1 B:ASN6 4.6 29.9 1.0
N B:GLY4 4.7 42.0 1.0
N B:ARG7 4.7 27.7 1.0
C B:LYS2 4.8 50.9 1.0
N B:LYS3 4.8 48.6 1.0
CB B:LYS3 4.8 48.0 1.0

Calcium binding site 5 out of 6 in 4ln1

Go back to Calcium Binding Sites List in 4ln1
Calcium binding site 5 out of 6 in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452


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 L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:37.6
occ:1.00
 OD1 C:ASP75 2.3 34.7 1.0
O C:LYS3 2.3 37.8 1.0
O C:ILE5 2.4 34.9 1.0
O C:HOH672 2.5 41.3 1.0
O C:HOH650 2.5 38.5 1.0
O C:HOH664 2.5 45.1 1.0
OD2 C:ASP75 2.5 32.7 1.0
O C:HOH655 2.6 37.4 1.0
CG C:ASP75 2.8 33.6 1.0
C C:LYS3 3.5 39.4 1.0
C C:ILE5 3.6 33.0 1.0
NH2 C:ARG280 4.2 41.3 1.0
CA C:LYS3 4.2 43.0 1.0
CB C:ASP75 4.3 33.2 1.0
N C:ILE5 4.3 33.9 1.0
C C:GLY4 4.3 34.2 1.0
CA C:ASN6 4.4 31.1 1.0
O C:ASP73 4.4 41.5 1.0
N C:ASN6 4.4 31.4 1.0
N C:GLY4 4.5 37.6 1.0
CA C:ILE5 4.6 33.6 1.0
CA C:GLY4 4.7 35.2 1.0
O C:GLY4 4.7 35.0 1.0
O C:HOH689 4.7 47.3 1.0
OD1 C:ASN6 4.7 33.6 1.0
N C:ARG7 4.8 30.6 1.0
O C:LYS2 4.8 43.2 1.0

Calcium binding site 6 out of 6 in 4ln1

Go back to Calcium Binding Sites List in 4ln1
Calcium binding site 6 out of 6 in the Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452


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 L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:43.3
occ:1.00
 O D:ILE5 2.3 34.0 1.0
OD1 D:ASP75 2.3 36.3 1.0
O D:LYS3 2.3 44.9 1.0
O D:HOH643 2.4 39.5 1.0
O D:HOH653 2.6 43.8 1.0
OD2 D:ASP75 2.6 34.6 1.0
O D:HOH674 2.6 53.2 1.0
O D:HOH670 2.7 39.9 1.0
CG D:ASP75 2.8 35.0 1.0
C D:LYS3 3.5 44.4 1.0
C D:ILE5 3.5 33.8 1.0
CA D:LYS3 4.2 45.7 1.0
N D:ILE5 4.2 36.1 1.0
CB D:ASP75 4.3 33.2 1.0
C D:GLY4 4.3 38.1 1.0
NH1 D:ARG280 4.4 39.2 1.0
N D:ASN6 4.4 32.5 1.0
CA D:ASN6 4.4 32.2 1.0
N D:GLY4 4.5 42.5 1.0
CA D:ILE5 4.5 35.2 1.0
O D:ASP73 4.5 43.1 1.0
O D:LYS2 4.6 49.0 1.0
O D:GLY4 4.7 39.0 1.0
O D:HOH682 4.7 49.0 1.0
CA D:GLY4 4.7 39.0 1.0
N D:ARG7 4.8 31.6 1.0
OD1 D:ASN6 4.9 33.0 1.0
CB D:LYS3 5.0 46.8 1.0

Reference:

V.N.Malashkevich, J.B.Bonanno, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garforth, A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.Lim, A.Celikgil, G.Villegas, B.Evans, J.Love, A.Fiser, K.Khafizov, R.Seidel, S.C.Almo. Crystal Structure of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579 Complexed with Calcium, Nysgrc Target 029452 To Be Published.
Page generated: Sun Jul 14 09:39:27 2024

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